Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
Nikulenkov, F, Spinnler, C, Li, H, Tonelli, C, Shi, Y, Turunen, M, Kivioja, T, Ignatiev, I, Kel, A, Taipale, J, Selivanova, G
Published in Cell death and differentiation (01.12.2012)
Published in Cell death and differentiation (01.12.2012)
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Journal Article
Optimization of cDNA-AFLP experiments using genomic sequence data
Kivioja, Teemu, Arvas, Mikko, Saloheimo, Markku, Penttilä, Merja, Ukkonen, Esko
Published in Bioinformatics (01.06.2005)
Published in Bioinformatics (01.06.2005)
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Journal Article
Data integration and visualization system for enabling conceptual biology
Gopalacharyulu, Peddinti V., Lindfors, Erno, Bounsaythip, Catherine, Kivioja, Teemu, Yetukuri, Laxman, Hollmén, Jaakko, Orešič, Matej
Published in Bioinformatics (01.06.2005)
Published in Bioinformatics (01.06.2005)
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Journal Article
DNA-dependent formation of transcription factor pairs alters their binding specificity
Jolma, Arttu, Yin, Yimeng, Nitta, Kazuhiro R., Dave, Kashyap, Popov, Alexander, Taipale, Minna, Enge, Martin, Kivioja, Teemu, Morgunova, Ekaterina, Taipale, Jussi
Published in Nature (London) (19.11.2015)
Published in Nature (London) (19.11.2015)
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Journal Article
Sequence determinants of human gene regulatory elements
Sahu, Biswajyoti, Hartonen, Tuomo, Pihlajamaa, Päivi, Wei, Bei, Dave, Kashyap, Zhu, Fangjie, Kaasinen, Eevi, Lidschreiber, Katja, Lidschreiber, Michael, Daub, Carsten O., Cramer, Patrick, Kivioja, Teemu, Taipale, Jussi
Published in Nature genetics (01.03.2022)
Published in Nature genetics (01.03.2022)
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Journal Article
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Yin, Yimeng, Morgunova, Ekaterina, Jolma, Arttu, Kaasinen, Eevi, Sahu, Biswajyoti, Khund-Sayeed, Syed, Das, Pratyush K., Kivioja, Teemu, Dave, Kashyap, Zhong, Fan, Nitta, Kazuhiro R., Taipale, Minna, Popov, Alexander, Ginno, Paul A., Domcke, Silvia, Yan, Jian, Schübeler, Dirk, Vinson, Charles, Taipale, Jussi
Published in Science (American Association for the Advancement of Science) (05.05.2017)
Published in Science (American Association for the Advancement of Science) (05.05.2017)
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Journal Article
Counting absolute numbers of molecules using unique molecular identifiers
Kivioja, Teemu, Vähärautio, Anna, Karlsson, Kasper, Bonke, Martin, Enge, Martin, Linnarsson, Sten, Taipale, Jussi
Published in Nature methods (01.01.2012)
Published in Nature methods (01.01.2012)
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Journal Article
Upregulation of ribosome biogenesis via canonical E-boxes is required for Myc-driven proliferation
Zielke, Norman, Vähärautio, Anna, Liu, Jianping, Kivioja, Teemu, Taipale, Jussi
Published in Developmental cell (25.04.2022)
Published in Developmental cell (25.04.2022)
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Journal Article
Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites
Yan, Jian, Enge, Martin, Whitington, Thomas, Dave, Kashyap, Liu, Jianping, Sur, Inderpreet, Schmierer, Bernhard, Jolma, Arttu, Kivioja, Teemu, Taipale, Minna, Taipale, Jussi
Published in Cell (15.08.2013)
Published in Cell (15.08.2013)
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Journal Article
DNA-Binding Specificities of Human Transcription Factors
Jolma, Arttu, Yan, Jian, Whitington, Thomas, Toivonen, Jarkko, Nitta, Kazuhiro R., Rastas, Pasi, Morgunova, Ekaterina, Enge, Martin, Taipale, Mikko, Wei, Gonghong, Palin, Kimmo, Vaquerizas, Juan M., Vincentelli, Renaud, Luscombe, Nicholas M., Hughes, Timothy R., Lemaire, Patrick, Ukkonen, Esko, Kivioja, Teemu, Taipale, Jussi
Published in Cell (2013)
Published in Cell (2013)
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Journal Article
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
Jolma, Arttu, Zhang, Jilin, Mondragón, Estefania, Morgunova, Ekaterina, Kivioja, Teemu, Laverty, Kaitlin U, Yin, Yimeng, Zhu, Fangjie, Bourenkov, Gleb, Morris, Quaid, Hughes, Timothy R, Maher, 3rd, Louis James, Taipale, Jussi
Published in Genome research (01.07.2020)
Published in Genome research (01.07.2020)
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Journal Article
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
Nitta, Kazuhiro R, Jolma, Arttu, Yin, Yimeng, Morgunova, Ekaterina, Kivioja, Teemu, Akhtar, Junaid, Hens, Korneel, Toivonen, Jarkko, Deplancke, Bart, Furlong, Eileen E M, Taipale, Jussi
Published in eLife (17.03.2015)
Published in eLife (17.03.2015)
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Journal Article
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Wei, Gong-Hong, Badis, Gwenael, Berger, Michael F, Kivioja, Teemu, Palin, Kimmo, Enge, Martin, Bonke, Martin, Jolma, Arttu, Varjosalo, Markku, Gehrke, Andrew R, Yan, Jian, Talukder, Shaheynoor, Turunen, Mikko, Taipale, Mikko, Stunnenberg, Hendrik G, Ukkonen, Esko, Hughes, Timothy R, Bulyk, Martha L, Taipale, Jussi
Published in The EMBO journal (07.07.2010)
Published in The EMBO journal (07.07.2010)
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Journal Article
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Jolma, Arttu, Kivioja, Teemu, Toivonen, Jarkko, Cheng, Lu, Wei, Gonghong, Enge, Martin, Taipale, Mikko, Vaquerizas, Juan M, Yan, Jian, Sillanpää, Mikko J, Bonke, Martin, Palin, Kimmo, Talukder, Shaheynoor, Hughes, Timothy R, Luscombe, Nicholas M, Ukkonen, Esko, Taipale, Jussi
Published in Genome research (01.06.2010)
Published in Genome research (01.06.2010)
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Journal Article
CRISPR/Cas9 screening using unique molecular identifiers
Schmierer, Bernhard, Botla, Sandeep K, Zhang, Jilin, Turunen, Mikko, Kivioja, Teemu, Taipale, Jussi
Published in Molecular systems biology (01.10.2017)
Published in Molecular systems biology (01.10.2017)
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Journal Article
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets
Toivonen, Jarkko, Kivioja, Teemu, Jolma, Arttu, Yin, Yimeng, Taipale, Jussi, Ukkonen, Esko
Published in Nucleic acids research (04.05.2018)
Published in Nucleic acids research (04.05.2018)
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Journal Article
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments
Hartonen, Tuomo, Sahu, Biswajyoti, Dave, Kashyap, Kivioja, Teemu, Taipale, Jussi
Published in BIOINFORMATICS (01.09.2016)
Published in BIOINFORMATICS (01.09.2016)
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Journal Article
Conference Proceeding
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility
Wei, Bei, Jolma, Arttu, Sahu, Biswajyoti, Orre, Lukas M, Zhong, Fan, Zhu, Fangjie, Kivioja, Teemu, Sur, Inderpreet, Lehtiö, Janne, Taipale, Minna, Taipale, Jussi
Published in Nature biotechnology (01.07.2018)
Published in Nature biotechnology (01.07.2018)
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Journal Article
Uterine Leiomyoma-Linked MED12 Mutations Disrupt Mediator-Associated CDK Activity
Turunen, Mikko, Spaeth, Jason M., Keskitalo, Salla, Park, Min Ju, Kivioja, Teemu, Clark, Alison D., Mäkinen, Netta, Gao, Fangjian, Palin, Kimmo, Nurkkala, Helka, Vähärautio, Anna, Aavikko, Mervi, Kämpjärvi, Kati, Vahteristo, Pia, Kim, Chongwoo A., Aaltonen, Lauri A., Varjosalo, Markku, Taipale, Jussi, Boyer, Thomas G.
Published in Cell reports (Cambridge) (08.05.2014)
Published in Cell reports (Cambridge) (08.05.2014)
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Journal Article