Genome Biology | Volume 10 Issue 4

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	Volume 10 Issue 4
	Comment
	Comment Guilt by association Gregory A Petsko Genome Biology 2009, 10:104 (29 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Given that the effectiveness of genome-wide association studies for finding disease genes is being debated, an alternative would be to look for diseases linked to inherited metabolic disorders.
	Review
	Minireview From transcription start site to cell biology Philipp Kapranov Genome Biology 2009, 10:217 (20 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNAs transcribed from previously unsuspected start sites add yet greater complexity to the mammalian transcriptome.
	Minireview Malaria sporozoite proteome leaves a trail Marissa Vignali, Cate Speake, Patrick E Duffy Genome Biology 2009, 10:216 (21 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the proteomes of malaria sporozoites at different stages and mutation of selected genes reveals proteins necessary for infection of the vertebrate host.
	Minireview Ribosomal footprints on a transcriptome landscape David R Morris Genome Biology 2009, 10:215 (28 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next-generation sequencing technology can be used to assess rates and regulation of translation across the entire yeast transcriptome.
	Opinion Back to Bermuda: how is science best served? Deanna M Church, LaDeana W Hillier Genome Biology 2009, 10:105 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
	Report
	Meeting report Genomic parasites and genome evolution Zoltán Ivics Genome Biology 2009, 10:306 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009.
	Meeting report Evolving proteins at Darwin's bicentenary John W Pinney, Michael PH Stumpf Genome Biology 2009, 10:307 (17 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 26-27 January 2009.
	Research
	Research Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii Nandita Mullapudi, Sandeep J Joseph, Jessica C Kissinger Genome Biology 2009, 10:R34 (7 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mining of genomic sequence data of the apicomplexan parasite Toxoplasma gondii identifies putative cis-regulatory elements using a de novo approach.
	Research Evolutionary rates and centrality in the yeast gene regulatory network Richard Jovelin, Patrick C Phillips Genome Biology 2009, 10:R35 (9 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Yeast transcription factors that are more central in the transcription network tend to evolve more quickly.
	Research The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes John W Whitaker, Glenn A McConkey, David R Westhead Genome Biology 2009, 10:R36 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metabolic network analysis in multiple eukaryotes identifies how horizontal and endosymbiotic gene transfer of metabolic enzyme-encoding genes leads to functional gene gain during evolution.
	Research Transcriptional features of genomic regulatory blocks Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten O Daub, Yoshihide Hayashizaki, Boris Lenhard Genome Biology 2009, 10:R38 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.
	Research Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki Genome Biology 2009, 10:R41 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Genome-wide analysis of EGR-1 binding sites reveals co-localization with CpG islands and histone H3 lysine 9 binding. SP-1 binding occupancies near EGR-1 binding sites are dramatically altered.
	Research A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.
	Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
	Research Microbial co-habitation and lateral gene transfer: what transposases can tell us Sean D Hooper, Konstantinos Mavromatis, Nikos C Kyrpides Genome Biology 2009, 10:R45 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interactions between microbial communities are revealed using a network of lateral gene transfer events.
	Method The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub Genome Biology 2009, 10:R40 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.
	Method Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data.
	Software Chromatin conformation signatures of cellular differentiation James Fraser, Mathieu Rousseau, Solomon Shenker, Maria A Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josée Dostie Genome Biology 2009, 10:R37 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A suite of computer programs to identify genome-wide chromatin conformation signatures with 5C technology is reported.
	Software FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub, Alistair RR Forrest Genome Biology 2009, 10:R39 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.

	Volume 10 Issue 4
	Comment
	Comment Guilt by association Gregory A Petsko Genome Biology 2009, 10:104 (29 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Given that the effectiveness of genome-wide association studies for finding disease genes is being debated, an alternative would be to look for diseases linked to inherited metabolic disorders.
	Review
	Minireview From transcription start site to cell biology Philipp Kapranov Genome Biology 2009, 10:217 (20 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RNAs transcribed from previously unsuspected start sites add yet greater complexity to the mammalian transcriptome.
	Minireview Malaria sporozoite proteome leaves a trail Marissa Vignali, Cate Speake, Patrick E Duffy Genome Biology 2009, 10:216 (21 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of the proteomes of malaria sporozoites at different stages and mutation of selected genes reveals proteins necessary for infection of the vertebrate host.
	Minireview Ribosomal footprints on a transcriptome landscape David R Morris Genome Biology 2009, 10:215 (28 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Next-generation sequencing technology can be used to assess rates and regulation of translation across the entire yeast transcriptome.
	Opinion Back to Bermuda: how is science best served? Deanna M Church, LaDeana W Hillier Genome Biology 2009, 10:105 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
	Report
	Meeting report Genomic parasites and genome evolution Zoltán Ivics Genome Biology 2009, 10:306 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009.
	Meeting report Evolving proteins at Darwin's bicentenary John W Pinney, Michael PH Stumpf Genome Biology 2009, 10:307 (17 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 26-27 January 2009.
	Research
	Research Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii Nandita Mullapudi, Sandeep J Joseph, Jessica C Kissinger Genome Biology 2009, 10:R34 (7 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Mining of genomic sequence data of the apicomplexan parasite Toxoplasma gondii identifies putative cis-regulatory elements using a de novo approach.
	Research Evolutionary rates and centrality in the yeast gene regulatory network Richard Jovelin, Patrick C Phillips Genome Biology 2009, 10:R35 (9 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Yeast transcription factors that are more central in the transcription network tend to evolve more quickly.
	Research The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes John W Whitaker, Glenn A McConkey, David R Westhead Genome Biology 2009, 10:R36 (15 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Metabolic network analysis in multiple eukaryotes identifies how horizontal and endosymbiotic gene transfer of metabolic enzyme-encoding genes leads to functional gene gain during evolution.
	Research Transcriptional features of genomic regulatory blocks Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten O Daub, Yoshihide Hayashizaki, Boris Lenhard Genome Biology 2009, 10:R38 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances.
	Research Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki Genome Biology 2009, 10:R41 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Genome-wide analysis of EGR-1 binding sites reveals co-localization with CpG islands and histone H3 lysine 9 binding. SP-1 binding occupancies near EGR-1 binding sites are dramatically altered.
	Research A whole-genome assembly of the domestic cow, Bos taurus Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg Genome Biology 2009, 10:R42 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A cow whole-genome assembly of 2.86 billion base pairs that closes gaps and corrects previously-described inversions and deletions as well as describing a portion of the Y chromosome.
	Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
	Research Microbial co-habitation and lateral gene transfer: what transposases can tell us Sean D Hooper, Konstantinos Mavromatis, Nikos C Kyrpides Genome Biology 2009, 10:R45 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Interactions between microbial communities are revealed using a network of lateral gene transfer events.
	Method The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub Genome Biology 2009, 10:R40 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.
	Method Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data.
	Software Chromatin conformation signatures of cellular differentiation James Fraser, Mathieu Rousseau, Solomon Shenker, Maria A Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josée Dostie Genome Biology 2009, 10:R37 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A suite of computer programs to identify genome-wide chromatin conformation signatures with 5C technology is reported.
	Software FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub, Alistair RR Forrest Genome Biology 2009, 10:R39 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.

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Volume 10 Issue 4

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