Genome Biology | Article collections

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, Carsten O Daub BMC Genomics 2010, 11:257 (21 April 2010)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation

Sebastian Schmeier, Cameron R MacPherson, Magbubah Essack, Mandeep Kaur, Ulf Schaefer, Harukazu Suzuki, Yoshihide Hayashizaki, Vladimir B Bajic BMC Genomics 2009, 10:595 (10 December 2009)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009)

Abstract | Full text | PDF | PubMed | Editor’s summary

The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence

Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential

Trinh Hoat, Nicolas Bertin, Noriko Ninomiya, Shiro Fukuda, Kengo Usui, Jun Kawai, Yoshihide Hayashizaki, Harukazu Suzuki BMC Cell Biology 2009, 10:69 (22 September 2009)

Abstract | Full text | PDF | PubMed

High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line

Naoki Adati, Ming-Chih Huang, Takahiro Suzuki, Harukazu Suzuki, Toshio Kojima BMC Research Notes 2009, 2:153 (27 July 2009)

Abstract | Full text | PDF | PubMed

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009)

A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

Hideya Kawaji, Yoshihide Hayashizaki, Carsten O Daub BMC Bioinformatics 2009, 10:133 (7 May 2009)

Abstract | Full text | PDF | PubMed

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)

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.

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)

The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.

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)

EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.

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)

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.

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)

A suite of computer programs to identify genome-wide chromatin conformation signatures with 5C technology is reported.

Data-driven normalization strategies for high-throughput quantitative RT-PCR

Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush BMC Bioinformatics 2009, 10:110 (19 April 2009)

Two new data-driven normalization strategies for high-throughput real-time quantitative PCR data directly correct for technical variation and offer advantages over existing normalization methods, which rely on comparisons with standard housekeeping genes.

		Research article Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, Carsten O Daub BMC Genomics 2010, 11:257 (21 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation Sebastian Schmeier, Cameron R MacPherson, Magbubah Essack, Mandeep Kaur, Ulf Schaefer, Harukazu Suzuki, Yoshihide Hayashizaki, Vladimir B Bajic BMC Genomics 2009, 10:595 (10 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence
		Methodology article Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential Trinh Hoat, Nicolas Bertin, Noriko Ninomiya, Shiro Fukuda, Kengo Usui, Jun Kawai, Yoshihide Hayashizaki, Harukazu Suzuki BMC Cell Biology 2009, 10:69 (22 September 2009) Abstract \| Full text \| PDF \| PubMed
		Short Report High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line Naoki Adati, Ming-Chih Huang, Takahiro Suzuki, Harukazu Suzuki, Toshio Kojima BMC Research Notes 2009, 2:153 (27 July 2009) Abstract \| Full text \| PDF \| PubMed
		Method Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen Genome Biology 2009, 10:R79 (22 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.
		Software SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes Hideya Kawaji, Yoshihide Hayashizaki, Carsten O Daub BMC Bioinformatics 2009, 10:133 (7 May 2009) Abstract \| Full text \| PDF \| PubMed
		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.
		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.
		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.
		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.
		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.
		Methodology article Data-driven normalization strategies for high-throughput quantitative RT-PCR Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush BMC Bioinformatics 2009, 10:110 (19 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two new data-driven normalization strategies for high-throughput real-time quantitative PCR data directly correct for technical variation and offer advantages over existing normalization methods, which rely on comparisons with standard housekeeping genes.

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