User profiles for T. Kivioja

Teemu Kivioja

University of Helsinki
Verified email at helsinki.fi
Cited by 8631

[HTML][HTML] DNA-binding specificities of human transcription factors

…, TR Hughes, P Lemaire, E Ukkonen, T Kivioja… - Cell, 2013 - cell.com
Although the proteins that read the gene regulatory code, transcription factors (TFs), have
been largely identified, it is not well known which sequences TFs can recognize. We have …

The EUROclass trial: defining subgroups in common variable immunodeficiency

…, T Kivioja, C Schmitt, B Ferry, T Witte… - Blood, The Journal …, 2008 - ashpublications.org
… Further analysis of lymphocyte subpopulations was restricted to total T cells, CD4 and CD8
T cells, as well as natural killer (NK) cells. Most patients have normal T-cell numbers (1204 ± …

Counting absolute numbers of molecules using unique molecular identifiers

T Kivioja, A Vähärautio, K Karlsson, M Bonke, M Enge… - Nature …, 2012 - nature.com
Counting individual RNA or DNA molecules is difficult because they are hard to copy
quantitatively for detection. To overcome this limitation, we applied unique molecular identifiers (…

Impact of cytosine methylation on DNA binding specificities of human transcription factors

…, B Sahu, S Khund-Sayeed, PK Das, T Kivioja… - Science, 2017 - science.org
INTRODUCTION Nearly all cells in the human body share the same primary genome sequence
consisting of four nucleotide bases. One of the bases, cytosine, is commonly modified by …

Genome‐wide analysis of ETS‐family DNA‐binding in vitro and in vivo

GH Wei, G Badis, MF Berger, T Kivioja, K Palin… - The EMBO …, 2010 - embopress.org
Members of the large ETS family of transcription factors (TFs) have highly similar DNA‐binding
domains (DBDs)—yet they have diverse functions and activities in physiology and …

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

A Jolma, T Kivioja, J Toivonen, L Cheng, G Wei… - Genome …, 2010 - genome.cshlp.org
The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary
structure is determined by DNA sequence. DNA also dictates when and where proteins are …

CTCF/cohesin-binding sites are frequently mutated in cancer

R Katainen, K Dave, E Pitkänen, K Palin, T Kivioja… - Nature …, 2015 - nature.com
… We found that the observed rate of A•T>C•G and A•T>G•C substitutions was significantly
higher than the expected rate (Supplementary Fig. 4 and Supplementary Table 3). Whereas in …

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

…, R Lehtonen, O Hallikas, S Vanharanta, T Kivioja… - Nature …, 2009 - nature.com
… functions as cofactor for transcription factors of the TCF (T-cell factor)/LEF (lymphoid enhancer
… We did not examine whether the imbalance is due to loss of the nonrisk T allele or gain of …

DNA-dependent formation of transcription factor pairs alters their binding specificity

…, K Dave, A Popov, M Taipale, M Enge, T Kivioja… - Nature, 2015 - nature.com
Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA
sequence motifs 1 , 2 , 3 . Such sequences are very common in the human genome, and …

[HTML][HTML] Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

…, K Dave, J Liu, I Sur, B Schmierer, A Jolma, T Kivioja… - Cell, 2013 - cell.com
During cell division, transcription factors (TFs) are removed from chromatin twice, during
DNA synthesis and during condensation of chromosomes. How TFs can efficiently find their …