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1
Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers
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Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers

Kwon, Andrew T ; Chou, Alice Yi ; Arenillas, David J ; Wasserman, Wyeth W Ponting, Chris P

PLoS computational biology, 2011-12, Vol.7 (12), p.e1002256-e1002256

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2
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
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JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Portales-Casamar, Elodie ; Thongjuea, Supat ; Kwon, Andrew T ; Arenillas, David ; Zhao, Xiaobei ; Valen, Eivind ; Yusuf, Dimas ; Lenhard, Boris ; Wasserman, Wyeth W ; Sandelin, Albin

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D105-D110 [Peer Reviewed Journal]

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3
Inference of transcriptional regulation relationships from gene expression data
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Inference of transcriptional regulation relationships from gene expression data

Kwon, Andrew T ; Hoos, Holger H ; Ng, Raymond

Bioinformatics (Oxford, England), 2003-05-22, Vol.19 (8), p.905-912 [Peer Reviewed Journal]

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4
Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation
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Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Morikawa, H ; Ohkura, N ; Vandenbon, A ; Itoh, M ; Nagao-Sato, S ; Kawaji, H ; Lassmann, T ; Carninci, P ; Hayashizaki, Y ; Forrest, A. R. R ; Standley, D. M ; Date, H ; Sakaguchi, S ; Rehli, M ; Baillie, J. K ; de Hoon, M. J. L ; Haberle, V ; Kulakovskiy, I. V ; Lizio, M ; Andersson, R ; Mungall, C. J ; Meehan, T. F ; Schmeier, S ; Bertin, N ; Jorgensen, M ; Dimont, E ; Arner, E ; Schmidl, C ; Schaefer, U ; Medvedeva, Y. A ; Plessy, C ; Vitezic, M ; Severin, J ; Semple, C. A ; Ishizu, Y ; Francescatto, M ; Alam, I ; Albanese, D ; Altschuler, G. M ; Archer, J. A. C ; Arner, P ; Babina, M ; Baker, S ; Balwierz, P. J ; Beckhouse, A. G ; Pradhan-Bhatt, S ; Blake, J. A ; Blumenthal, A ; Bodega, B ; Bonetti, A ; Briggs, J ; Brombacher, F ; Burroughs, A. M ; Califano, A ; Cannistraci, C. V ; Carbajo, D ; Chen, Y ; Chierici, M ; Ciani, Y ; Clevers, H. C ; Dalla, E ; Davis, C. A ; Deplancke, B ; Detmar, M ; Diehl, A. D ; Dohi, T ; Drablos, F ; Edge, A. S. B ; Edinger, M ; Ekwall, K ; Endoh, M ; Enomoto, H ; Fagiolini, M ; Fairbairn, L ; Fang, H ; Farach-Carson, M. C ; Faulkner, G. J ; Favorov, A. V ; Fisher, M. E ; Frith, M. C ; Fujita, R ; Fukuda, S ; Furlanello, C ; Furuno, M ; Furusawa, J.-i ; Geijtenbeek, T. B ; Gibson, A ; Gingeras, T ; Goldowitz, D ; Gough, J ; Guhl, S ; Guler, R ; Gustincich, S ; Ha, T. J ; Hamaguchi, M ; Hara, M ; Harbers, M ; Harshbarger, J ; Hasegawa, A ; Hasegawa, Y ; ...

Proceedings of the National Academy of Sciences - PNAS, 2014-03-27, Vol.111 (14), p.5289-5294 [Peer Reviewed Journal]

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5
An atlas of active enhancers across human cell types and tissues
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An atlas of active enhancers across human cell types and tissues

Andersson, Robin ; Gebhard, Claudia ; Miguel-Escalada, Irene ; Hoof, Ilka ; Bornholdt, Jette ; Boyd, Mette ; Chen, Yun ; Zhao, Xiaobei ; Schmidl, Christian ; Suzuki, Takahiro ; Ntini, Evgenia ; Arner, Erik ; Valen, Eivind ; Li, Kang ; Schwarzfischer, Lucia ; Glatz, Dagmar ; Raithel, Johanna ; Lilje, Berit ; Rapin, Nicolas ; Bagger, Frederik Otzen ; Jørgensen, Mette ; Andersen, Peter Refsing ; Bertin, Nicolas ; Rackham, Owen ; Burroughs, A. Maxwell ; Baillie, J. Kenneth ; Ishizu, Yuri ; Shimizu, Yuri ; Furuhata, Erina ; Maeda, Shiori ; Negishi, Yutaka ; Mungall, Christopher J ; Meehan, Terrence F ; Lassmann, Timo ; Itoh, Masayoshi ; Kawaji, Hideya ; Kondo, Naoto ; Kawai, Jun ; Lennartsson, Andreas ; Daub, Carsten O ; Heutink, Peter ; Hume, David A ; Jensen, Torben Heick ; Suzuki, Harukazu ; Hayashizaki, Yoshihide ; Müller, Ferenc ; Forrest, Alistair R. R ; Carninci, Piero ; Rehli, Michael ; Sandelin, Albin

Nature (London), 2014-03-26, Vol.507 (7493), p.455-461 [Peer Reviewed Journal]

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6
Ceruloplasmin Is a Novel Adipokine Which Is Overexpressed in Adipose Tissue of Obese Subjects and in Obesity-Associated Cancer Cells
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Ceruloplasmin Is a Novel Adipokine Which Is Overexpressed in Adipose Tissue of Obese Subjects and in Obesity-Associated Cancer Cells

Arner, Erik ; Forrest, Alistair R. R ; Ehrlund, Anna ; Mejhert, Niklas ; Itoh, Masayoshi ; Kawaji, Hideya ; Lassmann, Timo ; Laurencikiene, Jurga ; Rydén, Mikael ; Arner, Peter Wu, Qiong

PloS one, 2014-03-27, Vol.9 (3), p.e80274-e80274 [Peer Reviewed Journal]

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7
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome
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The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Hurst, Laurence D ; Ghanbarian, Avazeh T ; Forrest, Alistair R. R ; Huminiecki, Lukasz Barton, Nick H

PLoS biology, 2015-12-18, Vol.13 (12), p.e1002315-e1002315 [Peer Reviewed Journal]

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8
A promoter-level mammalian expression atlas
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A promoter-level mammalian expression atlas

Forrest, Alistair R. R ; Kawaji, Hideya ; Rehli, Michael ; Baillie, J. Kenneth ; de Hoon, Michiel J. L ; Haberle, Vanja ; Lassmann, Timo ; Kulakovskiy, Ivan V ; Lizio, Marina ; Itoh, Masayoshi ; Andersson, Robin ; Mungall, Christopher J ; Meehan, Terrence F ; Schmeier, Sebastian ; Bertin, Nicolas ; Jørgensen, Mette ; Dimont, Emmanuel ; Arner, Erik ; Schmidl, Christian ; Schaefer, Ulf ; Medvedeva, Yulia A ; Plessy, Charles ; Vitezic, Morana ; Severin, Jessica ; Semple, Colin A ; Ishizu, Yuri ; Young, Robert S ; Francescatto, Margherita ; Alam, Intikhab ; Albanese, Davide ; Altschuler, Gabriel M ; Arakawa, Takahiro ; Archer, John A. C ; Arner, Peter ; Babina, Magda ; Rennie, Sarah ; Balwierz, Piotr J ; Beckhouse, Anthony G ; Pradhan-Bhatt, Swati ; Blake, Judith A ; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessano ; Briggs, James ; Brombacher, Frank ; Burroughs, A. Maxwell ; Califano, Anea ; Cannistraci, Carlo V ; Geijtenbeek, Teunis B ; Gibson, Anew P

Nature (London), 2014-03-26, Vol.507 (7493), p.462-470 [Peer Reviewed Journal]

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9
CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes
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CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

Hasegawa, Yuki ; Tang, Dave ; Takahashi, Naoko ; Hayashizaki, Yoshihide ; Forrest, Alistair R. R ; Suzuki, Harukazu ; Kawaji, Hideya ; Rehli, Michael ; Baillie, J. Kenneth ; de Hoon, Michiel J. L ; Haberle, Vanja ; Lassmann, Timo ; Kulakovskiy, Ivan V ; Lizio, Marina ; Itoh, Masayoshi ; Andersson, Robin ; Mungall, Christopher J ; Meehan, Terrence F ; Schmeier, Sebastian ; Bertin, Nicolas ; Jørgensen, Mette ; Dimont, Emmanuel ; Arner, Erik ; Schmidl, Christian ; Schaefer, Ulf ; Medvedeva, Yulia A ; Plessy, Charles ; Vitezic, Morana ; Severin, Jessica ; Semple, Colin A ; Ishizu, Yuri ; Young, Robert S ; Francescatto, Margherita ; Alam, Intikhab ; Albanese, Davide ; Altschuler, Gabriel M ; Arakawa, Takahiro ; Archer, John A. C ; Arner, Peter ; Babina, Magda ; Baker, Sarah ; Balwierz, Piotr J ; Beckhouse, Anthony G ; Pradhan-Bhatt, Swati ; Blake, Judith A ; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessano ; Briggs, James ; Geijtenbeek, Teunis B

Scientific reports, 2014, Vol.4 (1), p.5228-5228 [Peer Reviewed Journal]

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10
oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets
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oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

Kwon, Andrew T ; Arenillas, David J ; Hunt, Rebecca Worsley ; Wasserman, Wyeth W

G3 (Bethesda, Md.), 2012-09, Vol.2 (9), p.987-1002

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