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2014 Journal Article Gene expression variability as a unifying element of the pluripotency networkMason, Elizabeth, Mar, Jessica C., Laslett, Andrew, Pera, Martin F., Quackenbush, John, Wolvetang, Ernst and Wells C. (2014). Gene expression variability as a unifying element of the pluripotency network. Stem Cell Reports, 3 (2), 365-377. doi: 10.1016/j.stemcr.2014.06.008 |
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2014 Journal Article Derivation of mesenchymal stromal cells from canine induced pluripotent stem cells by inhibition of the TGFbeta/activin signaling pathwayWhitworth, Deanne J., Frith, Jessica E, Frith, Thomas J. R., Ovchinnikov, Dmitry A., Cooper-White, Justin J. and Wolvetang, Ernst J. (2014). Derivation of mesenchymal stromal cells from canine induced pluripotent stem cells by inhibition of the TGFbeta/activin signaling pathway. Stem Cells and Development, Online Ahead of Print (24), 3021-3033. doi: 10.1089/scd.2013.0634 |
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2014 Journal Article CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genesHasegawa, Yuki, Tang, Dave, Takahashi, Naoko, Hayashizaki, Yoshihide, Forrest, Alistair R. R., the FANTOM consortium, Suzuki, Harukazu, Blumenthal, Antje, Kenna, Tony, Briggs, James, Beckhouse, Anthony G., Hitchens, Kelly J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014). CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports, 4 (Art No: 5228) 5228, 277-279. doi: 10.1038/srep05228 |
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2014 Journal Article Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenanceFort, Alexandre, Hashimoto, Kosuke, Yamada, Daisuke, Salimullah, Md, Keya, Chaman A., Saxena, Alka, Bonetti, Alessandro, Voineagu, Irina, Bertin, Nicolas, Kratz, Anton, Noro, Yukihiko, Wong, Chee-Hong, de Hoon, Michiel, Andersson, Robin, Sandelin, Albin, Suzuki, Harukazu, Wei, Chia-Lin, Koseki, Haruhiko, Hasegawa, Yuki, Forrest, Alistair R. R., Carninci, Piero, FANTOM Consortium, Beckhouse, Anthony, Blumenthal, Antje, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti ... Wolvetang, Ernst (2014). Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nature Genetics, 46 (6), 558-566. doi: 10.1038/ng.2965 |
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2014 Journal Article RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)Ohmiya, Hiroko, Vitezic, Morana, Frith, Martin C., Itoh, Masayoshi, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Lassmann, Timo, FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam, Kenna, Tony and Blumenthal, Antje (2014). RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics, 15 (1) 269. doi: 10.1186/1471-2164-15-269 |
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2014 Journal Article Redefinition of the human mast cell transcriptome by deep-CAGE sequencingMotakis, Efthymios, Guhl, Sven, Ishizu, Yuri, Itoh, Masayoshi, Kawaji, Hideya, de Hoon, Michiel, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Zuberbier, Torsten, Forrest, Alistair R. R., Babina, Magda, for The FANTOM Consortium, Wells, Christine, Wolvetang, Ernst, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (2014). Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 (17), 58-67. doi: 10.1182/blood-2013-02-483792 |
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2014 Journal Article High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesisPrasad, Punit, Rönnerblad, Michelle, Arner, Erik, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Daub, Carsten O., Forrest, Alistair R. R., Lennartsson, Andreas, Ekwall, Karl, for the FANTOM Consortium, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje and Kenna, Tony (2014). High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood, 123 (17), e46-e57. doi: 10.1182/blood-2013-02-483537 |
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2014 Journal Article The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulationsSchmidl, Christian, Hansmann, Leo, Lassmann, Timo, Balwierz, Piotr J., Kawaji, Hideya, Itoh, Masayoshi, Kawai, Jun, Nagao-Sato, Sayaka, Suzuki, Harukazu, Andreesen, Reinhard, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero, Hoffmann, Petra, Edinger, Matthias, Rehli, Michael, for the FANTOM consortium, Wells, Christine and Wolvetang, Ernst (2014). The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood, 123 (17), e68-e78. doi: 10.1182/blood-2013-02-486944 |
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2014 Journal Article Transcription and enhancer profiling in human monocyte subsetsSchmidl, Christian, Renner, Kathrin, Peter, Katrin, Eder, Ruediger, Lassmann, Timo, Balwierz, Piotr J., Itoh, Masayohshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Andreesen, Reinhard, Hume, David A., Hoffmann, Petra, Forrest, Alistair R. R., Kreutz, Marina P., Edinger, Matthias, Rehli, Michael, for the FANTOM consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Transcription and enhancer profiling in human monocyte subsets. Blood, 123 (17), e90-e99. doi: 10.1182/blood-2013-02-484188 |
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2014 Journal Article Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylationRönnerblad, Michelle, Andersson, Robin, Olofsson, Tor, Douagi, Iyadh, Karimi, Mohsen, Lehmann, Sören, Hoof, Ilka, de Hoon, Michiel, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Sandelin, Albin, Ekwall, Karl, Amer, Erik, Lennartsson, Andreas, for the FANTOM consortium, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Kenna, Tony, Hitchens, Kelly, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth ... Vijayan, Dipti (2014). Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood, 123 (17), e79-e89. doi: 10.1182/blood-2013-02-482893 |
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2014 Journal Article Interactive visualization and analysis of large-scale sequencing datasets using ZENBUSeverin, Jessica, Lizio, Marina, Harshbarger, Jayson, Kawaji, Hideya, Daub, Carsten O., Hayashizaki, Yoshihide, Bertin, Nicolas, Forrest, Alistair R. R., FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32 (3), 217-219. doi: 10.1038/nbt.2840 |
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2014 Journal Article Generation and characterization of leukemia inhibitory factor-dependent equine induced pluripotent stem cells from adult dermal fibroblastsWhitworth, Deanne J., Ovchinnikov, Dmitry A., Sun, Jane, Fortuna, Patrick R. J. and Wolvetang, Ernst J. (2014). Generation and characterization of leukemia inhibitory factor-dependent equine induced pluripotent stem cells from adult dermal fibroblasts. Stem Cells and Development, Fast Track Articles (13), 1-9. doi: 10.1089/scd.2013.0461 |
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2014 Journal Article Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like moleculesGrison, Alice, Zucchelli, Silvia, Urzi, Alice, Zamparo, Ilaria, Lazarevic, Dejan, Pascarella, Giovanni, Roncaglia, Paola, Giorgetti, Alejandro, Garcia-Esparcia, Paula, Vlachouli, Christina, Simone, Roberto, Persichetti, Francesca, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Carloni, Paolo, Ferrer, Isidro, Lodovichi, Claudia, Plessy, Charles, the FANTOM Consortium, Carninci, Piero, Gustincich, Stefano, Beckhouse, Anthony, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst ... Nielsen, Lars (2014). Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 (1) 729. doi: 10.1186/1471-2164-15-729 |
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2014 Journal Article A promoter-level mammalian expression atlasForest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, 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, Altschuler, Intikhab ... Hayashizaki, Yoshihide (2014). A promoter-level mammalian expression atlas. Nature, 507 (7493), 462-470. doi: 10.1038/nature13182 |
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2014 Journal Article A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiationTomaru, Yasuhiro, Hasegawa, Ryota, Suzuki, Takahiro, Sato, Taiji, Kubosaki, Atsutaka, Suzuki, Masanori, Kawaji, Hideya, Forrest, Alistair R. R., Hayashizaki, Yoshihide, FANTOM Consortium, Shin, Jay W., Suzuki, Harukazu, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Nucleic Acids Research, 42 (14), 8905-8913. doi: 10.1093/nar/gku567 |
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2014 Journal Article A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulatorsHurst, Laurence D., Sachenkova, Oxana, Daub, Carsten, Forrest, Alistair R. R., the FANTOM consortium, Huminiecki, Lukasz, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biology, 15 (7) 413. doi: 10.1186/s13059-014-0413-3 |
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2013 Journal Article Identification of Unsafe Human Induced Pluripotent Stem Cell Lines Using a Robust Surrogate Assay for PluripotencyPolanco, Juan Carlos, Ho, Mirabelle S. H., Wang, Bei, Zhou, Qi, Wolvetang, Ernst, Mason, Elizabeth, Wells, Christine A., Kolle, Gabriel, Grimmond, Sean M., Bertoncello, Ivan, O'Brien, Carmel and Laslett, Andrew L. (2013). Identification of Unsafe Human Induced Pluripotent Stem Cell Lines Using a Robust Surrogate Assay for Pluripotency. Stem Cells, 31 (8), 1498-1510. doi: 10.1002/stem.1425 |
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2013 Journal Article Full factorial screening of human embryonic stem cell maintenance with multiplexed microbioreactor arraysTitmarsh, Drew M., Ovchinnikov, Dmitry A., Wolvetang, Ernst J. and Cooper-White, Justin J. (2013). Full factorial screening of human embryonic stem cell maintenance with multiplexed microbioreactor arrays. Biotechnology Journal, 8 (7), 822-834. doi: 10.1002/biot.201200375 |
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2013 Journal Article Autophagy in stem cellsGuan, Jun-Lin, Simon, Anna Katharina, Prescott, Mark, Menendez, Javier A., Liu, Fei, Wang, Fen, Wang, Chenran, Wolvetang, Ernst, Vazquez-Martin, Alejandro and Zhang, Jue (2013). Autophagy in stem cells. Autophagy, 9 (6), 830-849. doi: 10.4161/auto.24132 |
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2013 Journal Article Concise review: new paradigms for down syndrome research using induced pluripotent stem cells: tackling complex human genetic diseaseBriggs, James A., Mason, Elizabeth A., Ovchinnikov, Dmitry A., Wells, Christine A. and Wolvetang, Ernst J. (2013). Concise review: new paradigms for down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. Stem Cells Translational Medicine, 2 (3), 175-184. doi: 10.5966/sctm.2012-0117 |
