T
Teemu Kivioja
Researcher at University of Helsinki
Publications - 48
Citations - 7344
Teemu Kivioja is an academic researcher from University of Helsinki. The author has contributed to research in topics: Gene & Transcription factor. The author has an hindex of 24, co-authored 45 publications receiving 6115 citations. Previous affiliations of Teemu Kivioja include National Institutes of Health & Karolinska Institutet.
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Journal ArticleDOI
DNA-Binding Specificities of Human Transcription Factors
Arttu Jolma,Jian Yan,Tom Whitington,Jarkko Toivonen,Kazuhiro R. Nitta,Pasi Rastas,Ekaterina Morgunova,Martin Enge,Mikko Taipale,Gong-Hong Wei,Kimmo Palin,Juan M. Vaquerizas,Renaud Vincentelli,Nicholas M. Luscombe,Timothy P. Hughes,Patrick Lemaire,Esko Ukkonen,Teemu Kivioja,Teemu Kivioja,Jussi Taipale,Jussi Taipale +20 more
TL;DR: Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated.
Journal ArticleDOI
Counting absolute numbers of molecules using unique molecular identifiers
Teemu Kivioja,Anna Vähärautio,Anna Vähärautio,Kasper Karlsson,Martin Bonke,Martin Enge,Sten Linnarsson,Jussi Taipale +7 more
TL;DR: Unique molecular identifiers (UMIs), which make each molecule in a population distinct, are applied to genome-scale human karyotyping and mRNA sequencing in Drosophila melanogaster to improve accuracy of almost any next-generation sequencing method.
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Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Yimeng Yin,Ekaterina Morgunova,Arttu Jolma,Eevi Kaasinen,Biswajyoti Sahu,Syed Khund-Sayeed,Pratyush Kumar Das,Teemu Kivioja,Kashyap Dave,Fan Zhong,Kazuhiro R. Nitta,Minna Taipale,Alexander Popov,Paul A. Ginno,Silvia Domcke,Silvia Domcke,Jian Yan,Dirk Schübeler,Dirk Schübeler,Charles Vinson,Jussi Taipale,Jussi Taipale +21 more
TL;DR: This work systematically analyzed binding specificities of full-length transcription factors and extended DNA binding domains to unmethylated and CpG-methylated DNA by using methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment).
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Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo
Gong-Hong Wei,Gwenael Badis,Michael F. Berger,Teemu Kivioja,Teemu Kivioja,Kimmo Palin,Martin Enge,Martin Bonke,Arttu Jolma,Markku Varjosalo,Andrew R. Gehrke,Jian Yan,Shaheynoor Talukder,Mikko P. Turunen,Mikko Taipale,Hendrik G. Stunnenberg,Esko Ukkonen,Timothy P. Hughes,Martha L. Bulyk,Jussi Taipale,Jussi Taipale +20 more
TL;DR: The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo, and this work identifies amino‐acid residues that are critical for the differences in specificity between all the classes.
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The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
Sari Tuupanen,Mikko P. Turunen,Rainer Lehtonen,Outi Hallikas,Sakari Vanharanta,Sakari Vanharanta,Teemu Kivioja,Mikael Björklund,Gong-Hong Wei,Jian Yan,Iina Niittymäki,Jukka-Pekka Mecklin,Heikki Järvinen,Ari Ristimäki,Ari Ristimäki,Mariachiara Di-Bernardo,Phil East,Luis G. Carvajal-Carmona,Richard S. Houlston,Ian Tomlinson,Kimmo Palin,Kimmo Palin,Esko Ukkonen,Auli Karhu,Jussi Taipale,Lauri A. Aaltonen +25 more
TL;DR: It is reported here that the risk allele G shows copy number increase during CRC development and provides evidence that the common CRC predisposition associated with 8q24 arises from enhanced responsiveness to Wnt signaling.