Genome Biology | Volume 9 Issue 2

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 9 Issue 2
	Comment
	Comment The right to be wrong Gregory A Petsko Genome Biology 2008, 9:102 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Nothing holds science back longer than clinging to what should not be clung to, and all too often it’s fear, fear of the consequences of having made a mistake, that keeps ideas around long past their expiration date.
	Review
	Review No evidence of a Neanderthal contribution to modern human diversity Jason A Hodgson, Todd R Disotell Genome Biology 2008, 9:206 (18 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies of genomic DNA from Neanderthal fossils support earlier studies showing no contribution of Neanderthals to the gene pool of modern humans.
	Protein family review The Argonaute protein family Julia Höck, Gunter Meister Genome Biology 2008, 9:210 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-guided gene silencing is mediated by proteins of the Argonaute family
	Minireview A systems view of Drosophila segmentation Mike Levine Genome Biology 2008, 9:207 (11 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned?
	Minireview Intron mis-splicing: no alternative? Scott Roy, Manuel Irimia Genome Biology 2008, 9:208 (19 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Eukaryotes compensate for inefficient splicing by mechanisms that prevent the translation of mis-spliced or unspliced mRNAs.
	Minireview Proteomic view of mitochondrial function Kai Dimmer, Doron Rapaport Genome Biology 2008, 9:209 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A screen for genes affecting mitochondrial function in Drosophila suggests that many modulators of mitochondrial function act outside the organelle.
	Report
	Meeting report In silico meets in vivo Zhiping Weng, Roderic Guigó Genome Biology 2008, 9:302 (25 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007.
	Research
	Research Do Alu repeats drive the evolution of the primate transcriptome? Araxi O Urrutia, Leandro Ocaña, Laurence D Hurst Genome Biology 2008, 9:R25 (1 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The abundance of Alu elements near broadly expressed genes is best explained by their preferential preservation near housekeeping genes.
	Research Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle Chava Yanay, Noa Morpurgo, Michal Linial Genome Biology 2008, 9:R27 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of human versus insects sheds light on the composition and assembly of protein complexes in the insect synapse.
	Research Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication Maria Cardone, Zhaoshi Jiang, Pietro D'Addabbo, Nicoletta Archidiacono, Mariano Rocchi, Evan E Eichler, Mario Ventura Genome Biology 2008, 9:R28 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A FISH analysis of chromosome 17 homologs in primates suggests that genomic architecture has a direct role in karyotype evolution and in the genomic instability associated with human disease.
	Research Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes Tobias Warnecke, Joanna L Parmley, Laurence D Hurst Genome Biology 2008, 9:R29 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Biased usage of amino acids near exon-intron boundaries is phylogenetically widespread and characteristic of species for which there are expected to be problems defining exons.
	Research Genomic degradation of a young Y chromosome in Drosophila miranda Doris Bachtrog, Emily Hom, Karen M Wong, Xulio Maside, Pieter de Jong Genome Biology 2008, 9:R30 (12 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Study of the recently formed neo-Y chromosome of Drosophila miranda demonstrate that degeneration of a recently formed Y-chromosome can proceed very rapidly.
	Research Text-mining assisted regulatory annotation Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium Genome Biology 2008, 9:R31 (13 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated cis-regulatory data.
	Research Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes Timothy E Cullingford, Thomais Markou, Stephen J Fuller, Alejandro Giraldo, Sampsa Pikkarainen, Georgia Zoumpoulidou, Ali Alsafi, Collins Ekere, Timothy J Kemp, Jayne L Dennis, Laurence Game, Peter H Sugden, Angela Clerk Genome Biology 2008, 9:R32 (14 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray profiling study of rat cardiomyocytes provides insights into early and second phase transcriptional responses induced by endothelin-1 and shows the importance of ERK1/2 signaling.
	Research Functional protein divergence in the evolution of Homo sapiens Nuria Lopez-Bigas, Subhajyoti De, Sarah A Teichmann Genome Biology 2008, 9:R33 (15 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quantification of the divergence of proteins by functional category shows that morphological changes in metazoa have been driven by variation in regulatory genes.
	Research Proteomic analysis of the secretome of Leishmania donovani J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster, Neil E Reiner Genome Biology 2008, 9:R35 (18 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of Leishmania-conditioned medium resulted in the identification of 151 proteins apparently secreted by the parasitic protozoan Leishmania donovani and suggested a vesicle-based secretion system.
	Research Sequence context affects the rate of short insertions and deletions in flies and primates Amos Tanay, Eric D Siggia Genome Biology 2008, 9:R37 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a large collection of short insertions and deletions in primates and flies shows that the rate of insertions or deletions of specific lengths can vary by more than 100 fold, depending on the surrounding sequence.
	Research Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia Li Wei Chang, Jacqueline E Payton, Wenlin Yuan, Timothy J Ley, Rakesh Nagarajan, Gary D Stormo Genome Biology 2008, 9:R38 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A dissection of the genetic networks and circuitries is described for two form of leukaemia. Integrating transcription factor binding and gene expression profiling, networks are revealed that underly this important human disease.
	Research Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes Hsiao-Pei Yang, Daniel A Barbash Genome Biology 2008, 9:R39 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evidence is presented that DINE-1 is a highly abundant miniature inverted-repeat transposable element (MITE) family present in all 12 Drosophila species with whole-genome sequence available.
	Research Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna Lars-Henrik Heckmann, Richard M Sibly, Richard Connon, Helen L Hooper, Thomas H Hutchinson, Steve J Maund, Christopher J Hill, Anthony Bouetard, Amanda Callaghan Genome Biology 2008, 9:R40 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of the transcriptomic and phenotypic stress responses of the model crustacean Daphnia magna following exposure to ibuprofen shows similarities in its mode of action between vertebrates and invertebrates.
	Research Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans Guanggan Hu, Iris Liu, Anita Sham, Jason E Stajich, Fred S Dietrich, James W Kronstad Genome Biology 2008, 9:R41 (22 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans is revealed through comparative genome hybridization between strains of different mating type, molecular subtype and ploidy.
	Research Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction Hans-Henrik Fuxelius, Alistair C Darby, Nam-Huyk Cho, Siv GE Andersson Genome Biology 2008, 9:R42 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Variably present genes and pseudogenes in Rickettsia species tend to have been acquired more recently and to be more divergent from the genes conserved across all species
	Research Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells Daniel R Rines, Maria Gomez-Ferreria, Yingyao Zhou, Paul DeJesus, Seanna Grob, Serge Batalov, Marc Labow, Dieter Huesken, Craig Mickanin, Jonathan Hall, Mischa Reinhardt, Francois Natt, Joerg Lange, David J Sharp, Sumit K Chanda, Jeremy S Caldwell Genome Biology 2008, 9:R44 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A loss-of-function screen for siRNAs that arrest human cells in metaphase reveals genes involved in mitotic spindle integrity.
	Method Correction of technical bias in clinical microarray data improves concordance with known biological information Aron C Eklund, Zoltan Szallasi Genome Biology 2008, 9:R26 (4 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to correct for technical bias in clinical microarray data, which increases concordance with known biological relationships.
	Method Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context Alexander E Kel, Monika Niehof, Volker Matys, Rüdiger Zemlin, Jürgen Borlak Genome Biology 2008, 9:R36 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An application of machine learning algorithms enables prediction of the functional context of transcription factor binding sites in the human genome.
	Method UTILLdb, a Pisum sativum in silico forward and reverse genetics tool Marion Dalmais, Julien Schmidt, Christine Le Signor, Francoise Moussy, Judith Burstin, Vincent Savois, Gregoire Aubert, Veronique Brunaud, Yannick de Oliveira, Cecile Guichard, Richard Thompson, Abdelhafid Bendahmane Genome Biology 2008, 9:R43 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UTILLdb is a database of phenotypic and sequence information on mutant genes from a reference Pisum sativum EMS-mutant population.
	Method Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza HyeRan Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Goicoechea, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund, Rod A Wing Genome Biology 2008, 9:R45 (28 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented
	Method SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays Miguel A Anton, Dorleta Gorostiaga, Elizabeth Guruceaga, Victor Segura, Pedro Carmona-Saez, Alberto Pascual-Montano, Ruben Pio, Luis M Montuenga, Angel Rubio Genome Biology 2008, 9:R46 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and ‘exon plus junction’ microarray data.
	Software Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes Pär G Engström, David Fredman, Boris Lenhard Genome Biology 2008, 9:R34 (15 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ancora is a web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements for multiple genomes.

	Volume 9 Issue 2
	Comment
	Comment The right to be wrong Gregory A Petsko Genome Biology 2008, 9:102 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Nothing holds science back longer than clinging to what should not be clung to, and all too often it’s fear, fear of the consequences of having made a mistake, that keeps ideas around long past their expiration date.
	Review
	Review No evidence of a Neanderthal contribution to modern human diversity Jason A Hodgson, Todd R Disotell Genome Biology 2008, 9:206 (18 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent studies of genomic DNA from Neanderthal fossils support earlier studies showing no contribution of Neanderthals to the gene pool of modern humans.
	Protein family review The Argonaute protein family Julia Höck, Gunter Meister Genome Biology 2008, 9:210 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNA-guided gene silencing is mediated by proteins of the Argonaute family
	Minireview A systems view of Drosophila segmentation Mike Levine Genome Biology 2008, 9:207 (11 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned?
	Minireview Intron mis-splicing: no alternative? Scott Roy, Manuel Irimia Genome Biology 2008, 9:208 (19 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Eukaryotes compensate for inefficient splicing by mechanisms that prevent the translation of mis-spliced or unspliced mRNAs.
	Minireview Proteomic view of mitochondrial function Kai Dimmer, Doron Rapaport Genome Biology 2008, 9:209 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A screen for genes affecting mitochondrial function in Drosophila suggests that many modulators of mitochondrial function act outside the organelle.
	Report
	Meeting report In silico meets in vivo Zhiping Weng, Roderic Guigó Genome Biology 2008, 9:302 (25 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007.
	Research
	Research Do Alu repeats drive the evolution of the primate transcriptome? Araxi O Urrutia, Leandro Ocaña, Laurence D Hurst Genome Biology 2008, 9:R25 (1 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The abundance of Alu elements near broadly expressed genes is best explained by their preferential preservation near housekeeping genes.
	Research Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle Chava Yanay, Noa Morpurgo, Michal Linial Genome Biology 2008, 9:R27 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of human versus insects sheds light on the composition and assembly of protein complexes in the insect synapse.
	Research Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication Maria Cardone, Zhaoshi Jiang, Pietro D'Addabbo, Nicoletta Archidiacono, Mariano Rocchi, Evan E Eichler, Mario Ventura Genome Biology 2008, 9:R28 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A FISH analysis of chromosome 17 homologs in primates suggests that genomic architecture has a direct role in karyotype evolution and in the genomic instability associated with human disease.
	Research Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes Tobias Warnecke, Joanna L Parmley, Laurence D Hurst Genome Biology 2008, 9:R29 (7 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Biased usage of amino acids near exon-intron boundaries is phylogenetically widespread and characteristic of species for which there are expected to be problems defining exons.
	Research Genomic degradation of a young Y chromosome in Drosophila miranda Doris Bachtrog, Emily Hom, Karen M Wong, Xulio Maside, Pieter de Jong Genome Biology 2008, 9:R30 (12 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Study of the recently formed neo-Y chromosome of Drosophila miranda demonstrate that degeneration of a recently formed Y-chromosome can proceed very rapidly.
	Research Text-mining assisted regulatory annotation Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium Genome Biology 2008, 9:R31 (13 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated cis-regulatory data.
	Research Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes Timothy E Cullingford, Thomais Markou, Stephen J Fuller, Alejandro Giraldo, Sampsa Pikkarainen, Georgia Zoumpoulidou, Ali Alsafi, Collins Ekere, Timothy J Kemp, Jayne L Dennis, Laurence Game, Peter H Sugden, Angela Clerk Genome Biology 2008, 9:R32 (14 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray profiling study of rat cardiomyocytes provides insights into early and second phase transcriptional responses induced by endothelin-1 and shows the importance of ERK1/2 signaling.
	Research Functional protein divergence in the evolution of Homo sapiens Nuria Lopez-Bigas, Subhajyoti De, Sarah A Teichmann Genome Biology 2008, 9:R33 (15 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quantification of the divergence of proteins by functional category shows that morphological changes in metazoa have been driven by variation in regulatory genes.
	Research Proteomic analysis of the secretome of Leishmania donovani J Maxwell Silverman, Simon K Chan, Dale P Robinson, Dennis M Dwyer, Devki Nandan, Leonard J Foster, Neil E Reiner Genome Biology 2008, 9:R35 (18 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of Leishmania-conditioned medium resulted in the identification of 151 proteins apparently secreted by the parasitic protozoan Leishmania donovani and suggested a vesicle-based secretion system.
	Research Sequence context affects the rate of short insertions and deletions in flies and primates Amos Tanay, Eric D Siggia Genome Biology 2008, 9:R37 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of a large collection of short insertions and deletions in primates and flies shows that the rate of insertions or deletions of specific lengths can vary by more than 100 fold, depending on the surrounding sequence.
	Research Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia Li Wei Chang, Jacqueline E Payton, Wenlin Yuan, Timothy J Ley, Rakesh Nagarajan, Gary D Stormo Genome Biology 2008, 9:R38 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A dissection of the genetic networks and circuitries is described for two form of leukaemia. Integrating transcription factor binding and gene expression profiling, networks are revealed that underly this important human disease.
	Research Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes Hsiao-Pei Yang, Daniel A Barbash Genome Biology 2008, 9:R39 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Evidence is presented that DINE-1 is a highly abundant miniature inverted-repeat transposable element (MITE) family present in all 12 Drosophila species with whole-genome sequence available.
	Research Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna Lars-Henrik Heckmann, Richard M Sibly, Richard Connon, Helen L Hooper, Thomas H Hutchinson, Steve J Maund, Christopher J Hill, Anthony Bouetard, Amanda Callaghan Genome Biology 2008, 9:R40 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A study of the transcriptomic and phenotypic stress responses of the model crustacean Daphnia magna following exposure to ibuprofen shows similarities in its mode of action between vertebrates and invertebrates.
	Research Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans Guanggan Hu, Iris Liu, Anita Sham, Jason E Stajich, Fred S Dietrich, James W Kronstad Genome Biology 2008, 9:R41 (22 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans is revealed through comparative genome hybridization between strains of different mating type, molecular subtype and ploidy.
	Research Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction Hans-Henrik Fuxelius, Alistair C Darby, Nam-Huyk Cho, Siv GE Andersson Genome Biology 2008, 9:R42 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Variably present genes and pseudogenes in Rickettsia species tend to have been acquired more recently and to be more divergent from the genes conserved across all species
	Research Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells Daniel R Rines, Maria Gomez-Ferreria, Yingyao Zhou, Paul DeJesus, Seanna Grob, Serge Batalov, Marc Labow, Dieter Huesken, Craig Mickanin, Jonathan Hall, Mischa Reinhardt, Francois Natt, Joerg Lange, David J Sharp, Sumit K Chanda, Jeremy S Caldwell Genome Biology 2008, 9:R44 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A loss-of-function screen for siRNAs that arrest human cells in metaphase reveals genes involved in mitotic spindle integrity.
	Method Correction of technical bias in clinical microarray data improves concordance with known biological information Aron C Eklund, Zoltan Szallasi Genome Biology 2008, 9:R26 (4 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is presented to correct for technical bias in clinical microarray data, which increases concordance with known biological relationships.
	Method Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context Alexander E Kel, Monika Niehof, Volker Matys, Rüdiger Zemlin, Jürgen Borlak Genome Biology 2008, 9:R36 (21 February 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An application of machine learning algorithms enables prediction of the functional context of transcription factor binding sites in the human genome.
	Method UTILLdb, a Pisum sativum in silico forward and reverse genetics tool Marion Dalmais, Julien Schmidt, Christine Le Signor, Francoise Moussy, Judith Burstin, Vincent Savois, Gregoire Aubert, Veronique Brunaud, Yannick de Oliveira, Cecile Guichard, Richard Thompson, Abdelhafid Bendahmane Genome Biology 2008, 9:R43 (26 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary UTILLdb is a database of phenotypic and sequence information on mutant genes from a reference Pisum sativum EMS-mutant population.
	Method Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza HyeRan Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Goicoechea, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund, Rod A Wing Genome Biology 2008, 9:R45 (28 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented
	Method SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays Miguel A Anton, Dorleta Gorostiaga, Elizabeth Guruceaga, Victor Segura, Pedro Carmona-Saez, Alberto Pascual-Montano, Ruben Pio, Luis M Montuenga, Angel Rubio Genome Biology 2008, 9:R46 (29 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SPACE is an algorithm developed to predict and quantify the pre-mRNA splicing structure of transcripts using exon and ‘exon plus junction’ microarray data.
	Software Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes Pär G Engström, David Fredman, Boris Lenhard Genome Biology 2008, 9:R34 (15 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ancora is a web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements for multiple genomes.

Explore Genome Biology

Articles

Volume 9 Issue 2

Comment

Review

Report

Research