Genome Biology | Volume 9 Issue 3

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	Volume 9 Issue 3
	Comment
	Comment Going to the dogs Gregory A Petsko Genome Biology 2008, 9:103 (31 March 2008) Abstract \| Full text \| PDF \| Editor’s summary In the age of genomics, when biology is becoming more quantitative and depending more on new techniques and tools that must come from the physical sciences most biologists can't understand chemists and physicists and hardly any chemists and physicists know what to make of the typical biology seminar.
	Review
	Review Innate recognition of non-self nucleic acids Hongbo Chi, Richard A Flavell Genome Biology 2008, 9:211 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A variety of innate immune system receptors recognize and respond to the nucleic acids of invading pathogens.
	Minireview On the nature of thumbs Günter P Wagner, Alexander O Vargas Genome Biology 2008, 9:213 (4 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Differential Hox gene expression make the thumb special.
	Minireview Cytoplasmic dynein could be key to understanding neurodegeneration Gareth T Banks, Elizabeth MC Fisher Genome Biology 2008, 9:214 (28 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new mouse mutant uncovers an essential role of cytoplasmic dyenin in sensory nervous system.
	Minireview Bilateral olfaction: two is better than one for navigation Baranidharan Raman, Iori Ito, Mark Stopfer Genome Biology 2008, 9:212 (31 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila larvae with a single sense organ locate a source of odor as well as larvae with two.
	Research
	Research Functions, structure, and read-through alternative splicing of feline APOBEC3 genes Carsten Münk, Thomas Beck, Jörg Zielonka, Agnes Hotz-Wagenblatt, Sarah Chareza, Marion Battenberg, Jens Thielebein, Klaus Cichutek, Ignacio G Bravo, Stephen J O'Brien, Martin Lochelt, Naoya Yuhki Genome Biology 2008, 9:R48 (3 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary APOBEC3 (A3, Apolipoprotein B mRNA-editing catalytic polypeptide 3) genes in the genome of domestic cat (Felis catus) were identified and characterized
	Research Analysis of 142 genes resolves the rapid diversification of the rice genus Xin-Hui Zou, Fu-Min Zhang, Jian-Guo Zhang, Li-Li Zang, Liang Tang, Jun Wang, Tao Sang, Song Ge Genome Biology 2008, 9:R49 (3 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The relationships among all diploid genome types of the rice genus were clarified using 142 single-copy genes
	Research Cross-kingdom patterns of alternative splicing and splice recognition Abigail M McGuire, Matthew D Pearson, Daniel E Neafsey, James E Galagan Genome Biology 2008, 9:R50 (5 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.
	Research Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks Ádám Kun, Balázs Papp, Eörs Szathmáry Genome Biology 2008, 9:R51 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Small-molecular metabolic autocatalytic regulators, which are crucial to metabolic pathways, are identified in a novel systems-wide study in different organisms, revealing that in the enzymatic reactions of conserved autocatalytic cycles, the autocatalytic behavior of replicators varies.
	Research Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status Bin Yan, Guang Chen, Kunal Saigal, Xinping Yang, Shane T Jensen, Carter Van Waes, Christian J Stoeckert, Zhong Chen Genome Biology 2008, 9:R53 (11 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Detailed analysis of NFκB regulons in 1,265 genes differentially expressed in head and neck cancer cell lines differing in p53 status revealed a cross talk between NFkB and specific signaling pathways.
	Research Functional diversification of duplicate genes through subcellular adaptation of encoded proteins Ana C Marques, Nicolas Vinckenbosch, David Brawand, Henrik Kaessmann Genome Biology 2008, 9:R54 (12 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the subcellular localization patterns of duplicate genes revealed that protein subcellular adaptation represents a common mechanism for the functional diversification of duplicate genes.
	Research Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays Lei Li, Hang He, Juan Zhang, Xiangfeng Wang, Sulan Bai, Viktor Stolc, Waraporn Tongprasit, Nevin D Young, Oliver Yu, Xing-Wang Deng Genome Biology 2008, 9:R57 (19 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The comparative transcriptional analysis of highly syntenic regions in six different organ types between Medicago truncatula (barrel medic) and Glycine max (soybean), using nucleotide tiling microarrays, provides insights into genome organization and transcriptional regulation in these legume plants.
	Research A sequence-based survey of the complex structural organization of tumor genomes Benjamin J Raphael, Stanislav Volik, Peng Yu, Chunxiao Wu, Guiqing Huang, Elena V Linardopoulou, Barbara J Trask, Frederic Waldman, Joseph Costello, Kenneth J Pienta, Gordon B Mills, Krystyna Bajsarowicz, Yasuko Kobayashi, Shivaranjani Sridharan, Pamela L Paris, Quanzhou Tao, Sarah J Aerni, Raymond P Brown, Ali Bashir, Joe W Gray, Jan-Fang Cheng, Pieter de Jong, Mikhail Nefedov, Thomas Ried, Hesed M Padilla-Nash, Colin C Collins Genome Biology 2008, 9:R59 (25 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tumors and cancer cell lines were surveyed with end-sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent.
	Research The impact of the neisserial DNA uptake sequences on genome evolution and stability Todd J Treangen, Ole Ambur, Tone Tonjum, Eduardo PC Rocha Genome Biology 2008, 9:R60 (26 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the origin and distribution of the abundant short DNA uptake sequence (DUS) in six genomes of Neisseria suggests that transformation and recombination are tightly linked in evolution and that recombination has a key role in the establishment of DUS.
	Research Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome Suzhi Wang, Marcé D Lorenzen, Richard W Beeman, Susan J Brown Genome Biology 2008, 9:R61 (26 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Approximately 30% of the Tribolium castaneum genome is comprised of repetitive DNA. These repeats accumulate in certain regions in the assembled T. castaneum genome, these regions might be derived from the large blocks of pericentric heterochromatin in Tribolium chromosomes.
	Research Reduced reliance on the trace element selenium during evolution of mammals Alexey V Lobanov, Dolph L Hatfield, Vadim N Gladyshev Genome Biology 2008, 9:R62 (31 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolution from fish to mammals was accompanied by decreased use of selenocysteine, raising questions about the need for selenium dietary supplements when pathology is not imminent.
	Method Gene expression-based screening for inhibitors of PDGFR signaling Alena A Antipova, Brent R Stockwell, Todd R Golub Genome Biology 2008, 9:R47 (1 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Inhibitors of the platelet derived growth factor receptor (PDGFR) signaling pathway are isolated using gene expression-based high-throughput screening (GE-HTS), a method that is applicable to other pathways.
	Method Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments Karuppasamy Manikandan, Debnath Pal, Suryanarayanarao Ramakumar, Nathan E Brener, Sitharama S Iyengar, Guna Seetharaman Genome Biology 2008, 9:R52 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A geometric clustering algorithm has been developed to dissect protein fragments based on their relevance to function.
	Method DNA signatures for detecting genetic engineering in bacteria Jonathan E Allen, Shea N Gardner, Tom R Slezak Genome Biology 2008, 9:R56 (18 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New computational tools were used to find a robust set of DNA oligomers that can distinguish artificial vector sequences from all available background viral and bacterial genomes.
	Method Indirect genomic effects on survival from gene expression data Egil Ferkingstad, Arnoldo Frigessi, Heidi Lyng Genome Biology 2008, 9:R58 (22 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel methodology is presented for detecting and quantifying indirect effects on cancer survival mediated through several target genes of transcription factors in cancer microarray data.
	Software Genome assembly forensics: finding the elusive mis-assembly Adam M Phillippy, Michael C Schatz, Mihai Pop Genome Biology 2008, 9:R55 (14 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A collection of software tools is combined for the first time in an automated pipeline for detecting large-scale genome assembly errors and for validating genome assemblies.
	Correspondence
	Correspondence The Amborella genome: an evolutionary reference for plant biology Douglas E Soltis, Victor A Albert, Jim Leebens-Mack, Jeffrey D Palmer, Rod A Wing, Claude W dePamphilis, Hong Ma, John E Carlson, Naomi Altman, Sangtae Kim, P Kerr Wall, Andrea Zuccolo, Pamela S Soltis Genome Biology 2008, 9:402 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.

	Volume 9 Issue 3
	Comment
	Comment Going to the dogs Gregory A Petsko Genome Biology 2008, 9:103 (31 March 2008) Abstract \| Full text \| PDF \| Editor’s summary In the age of genomics, when biology is becoming more quantitative and depending more on new techniques and tools that must come from the physical sciences most biologists can't understand chemists and physicists and hardly any chemists and physicists know what to make of the typical biology seminar.
	Review
	Review Innate recognition of non-self nucleic acids Hongbo Chi, Richard A Flavell Genome Biology 2008, 9:211 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A variety of innate immune system receptors recognize and respond to the nucleic acids of invading pathogens.
	Minireview On the nature of thumbs Günter P Wagner, Alexander O Vargas Genome Biology 2008, 9:213 (4 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Differential Hox gene expression make the thumb special.
	Minireview Cytoplasmic dynein could be key to understanding neurodegeneration Gareth T Banks, Elizabeth MC Fisher Genome Biology 2008, 9:214 (28 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new mouse mutant uncovers an essential role of cytoplasmic dyenin in sensory nervous system.
	Minireview Bilateral olfaction: two is better than one for navigation Baranidharan Raman, Iori Ito, Mark Stopfer Genome Biology 2008, 9:212 (31 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Drosophila larvae with a single sense organ locate a source of odor as well as larvae with two.
	Research
	Research Functions, structure, and read-through alternative splicing of feline APOBEC3 genes Carsten Münk, Thomas Beck, Jörg Zielonka, Agnes Hotz-Wagenblatt, Sarah Chareza, Marion Battenberg, Jens Thielebein, Klaus Cichutek, Ignacio G Bravo, Stephen J O'Brien, Martin Lochelt, Naoya Yuhki Genome Biology 2008, 9:R48 (3 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary APOBEC3 (A3, Apolipoprotein B mRNA-editing catalytic polypeptide 3) genes in the genome of domestic cat (Felis catus) were identified and characterized
	Research Analysis of 142 genes resolves the rapid diversification of the rice genus Xin-Hui Zou, Fu-Min Zhang, Jian-Guo Zhang, Li-Li Zang, Liang Tang, Jun Wang, Tao Sang, Song Ge Genome Biology 2008, 9:R49 (3 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The relationships among all diploid genome types of the rice genus were clarified using 142 single-copy genes
	Research Cross-kingdom patterns of alternative splicing and splice recognition Abigail M McGuire, Matthew D Pearson, Daniel E Neafsey, James E Galagan Genome Biology 2008, 9:R50 (5 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.
	Research Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks Ádám Kun, Balázs Papp, Eörs Szathmáry Genome Biology 2008, 9:R51 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Small-molecular metabolic autocatalytic regulators, which are crucial to metabolic pathways, are identified in a novel systems-wide study in different organisms, revealing that in the enzymatic reactions of conserved autocatalytic cycles, the autocatalytic behavior of replicators varies.
	Research Systems biology-defined NF-κB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status Bin Yan, Guang Chen, Kunal Saigal, Xinping Yang, Shane T Jensen, Carter Van Waes, Christian J Stoeckert, Zhong Chen Genome Biology 2008, 9:R53 (11 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Detailed analysis of NFκB regulons in 1,265 genes differentially expressed in head and neck cancer cell lines differing in p53 status revealed a cross talk between NFkB and specific signaling pathways.
	Research Functional diversification of duplicate genes through subcellular adaptation of encoded proteins Ana C Marques, Nicolas Vinckenbosch, David Brawand, Henrik Kaessmann Genome Biology 2008, 9:R54 (12 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the subcellular localization patterns of duplicate genes revealed that protein subcellular adaptation represents a common mechanism for the functional diversification of duplicate genes.
	Research Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays Lei Li, Hang He, Juan Zhang, Xiangfeng Wang, Sulan Bai, Viktor Stolc, Waraporn Tongprasit, Nevin D Young, Oliver Yu, Xing-Wang Deng Genome Biology 2008, 9:R57 (19 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The comparative transcriptional analysis of highly syntenic regions in six different organ types between Medicago truncatula (barrel medic) and Glycine max (soybean), using nucleotide tiling microarrays, provides insights into genome organization and transcriptional regulation in these legume plants.
	Research A sequence-based survey of the complex structural organization of tumor genomes Benjamin J Raphael, Stanislav Volik, Peng Yu, Chunxiao Wu, Guiqing Huang, Elena V Linardopoulou, Barbara J Trask, Frederic Waldman, Joseph Costello, Kenneth J Pienta, Gordon B Mills, Krystyna Bajsarowicz, Yasuko Kobayashi, Shivaranjani Sridharan, Pamela L Paris, Quanzhou Tao, Sarah J Aerni, Raymond P Brown, Ali Bashir, Joe W Gray, Jan-Fang Cheng, Pieter de Jong, Mikhail Nefedov, Thomas Ried, Hesed M Padilla-Nash, Colin C Collins Genome Biology 2008, 9:R59 (25 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tumors and cancer cell lines were surveyed with end-sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent.
	Research The impact of the neisserial DNA uptake sequences on genome evolution and stability Todd J Treangen, Ole Ambur, Tone Tonjum, Eduardo PC Rocha Genome Biology 2008, 9:R60 (26 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the origin and distribution of the abundant short DNA uptake sequence (DUS) in six genomes of Neisseria suggests that transformation and recombination are tightly linked in evolution and that recombination has a key role in the establishment of DUS.
	Research Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome Suzhi Wang, Marcé D Lorenzen, Richard W Beeman, Susan J Brown Genome Biology 2008, 9:R61 (26 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Approximately 30% of the Tribolium castaneum genome is comprised of repetitive DNA. These repeats accumulate in certain regions in the assembled T. castaneum genome, these regions might be derived from the large blocks of pericentric heterochromatin in Tribolium chromosomes.
	Research Reduced reliance on the trace element selenium during evolution of mammals Alexey V Lobanov, Dolph L Hatfield, Vadim N Gladyshev Genome Biology 2008, 9:R62 (31 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evolution from fish to mammals was accompanied by decreased use of selenocysteine, raising questions about the need for selenium dietary supplements when pathology is not imminent.
	Method Gene expression-based screening for inhibitors of PDGFR signaling Alena A Antipova, Brent R Stockwell, Todd R Golub Genome Biology 2008, 9:R47 (1 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Inhibitors of the platelet derived growth factor receptor (PDGFR) signaling pathway are isolated using gene expression-based high-throughput screening (GE-HTS), a method that is applicable to other pathways.
	Method Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments Karuppasamy Manikandan, Debnath Pal, Suryanarayanarao Ramakumar, Nathan E Brener, Sitharama S Iyengar, Guna Seetharaman Genome Biology 2008, 9:R52 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A geometric clustering algorithm has been developed to dissect protein fragments based on their relevance to function.
	Method DNA signatures for detecting genetic engineering in bacteria Jonathan E Allen, Shea N Gardner, Tom R Slezak Genome Biology 2008, 9:R56 (18 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New computational tools were used to find a robust set of DNA oligomers that can distinguish artificial vector sequences from all available background viral and bacterial genomes.
	Method Indirect genomic effects on survival from gene expression data Egil Ferkingstad, Arnoldo Frigessi, Heidi Lyng Genome Biology 2008, 9:R58 (22 March 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel methodology is presented for detecting and quantifying indirect effects on cancer survival mediated through several target genes of transcription factors in cancer microarray data.
	Software Genome assembly forensics: finding the elusive mis-assembly Adam M Phillippy, Michael C Schatz, Mihai Pop Genome Biology 2008, 9:R55 (14 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A collection of software tools is combined for the first time in an automated pipeline for detecting large-scale genome assembly errors and for validating genome assemblies.
	Correspondence
	Correspondence The Amborella genome: an evolutionary reference for plant biology Douglas E Soltis, Victor A Albert, Jim Leebens-Mack, Jeffrey D Palmer, Rod A Wing, Claude W dePamphilis, Hong Ma, John E Carlson, Naomi Altman, Sangtae Kim, P Kerr Wall, Andrea Zuccolo, Pamela S Soltis Genome Biology 2008, 9:402 (10 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.

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Articles

Volume 9 Issue 3

Comment

Review

Research

Correspondence