Teemu Kivioja

Teemu Kivioja

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Teemu Kivioja

Teemu Kivioja

Publications by authors named "Teemu Kivioja"

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29Publications

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A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.

Nat Biotechnol 2018 07 21;36(6):521-529. Epub 2018 May 21.

Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nbt.4138DOI Listing
July 2018

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.

Nucleic Acids Res 2018 05;46(8):e44

Department of Computer Science, P.O. Box 68, FI-00014 University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gky027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934673PMC
May 2018

CRISPR/Cas9 screening using unique molecular identifiers.

Mol Syst Biol 2017 10 9;13(10):945. Epub 2017 Oct 9.

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658704PMC
http://dx.doi.org/10.15252/msb.20177834DOI Listing
October 2017

PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments.

Bioinformatics 2016 09;32(17):i629-i638

Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btw448DOI Listing
September 2016

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

Nature 2015 Nov 9;527(7578):384-8. Epub 2015 Nov 9.

Department of Biosciences and Nutrition, Karolinska Institutet, SE 141 83, Sweden.

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http://dx.doi.org/10.1038/nature15518DOI Listing
November 2015

CTCF/cohesin-binding sites are frequently mutated in cancer.

Nat Genet 2015 Jul 8;47(7):818-21. Epub 2015 Jun 8.

1] Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland. [2] Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1038/ng.3335DOI Listing
July 2015

Uterine leiomyoma-linked MED12 mutations disrupt mediator-associated CDK activity.

Cell Rep 2014 May 18;7(3):654-60. Epub 2014 Apr 18.

Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, Mail Code 8257, STRF, San Antonio, TX 78229-3900, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.03.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041330PMC
May 2014

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.

Cell 2013 Aug;154(4):801-13

Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 14183, Sweden.

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http://dx.doi.org/10.1016/j.cell.2013.07.034DOI Listing
August 2013

Transcriptional networks controlling the cell cycle.

G3 (Bethesda) 2013 Jan 1;3(1):75-90. Epub 2013 Jan 1.

Genome-Scale Biology Research Program, Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1534/g3.112.004283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538345PMC
January 2013

Identification and characterization of gushing-active hydrophobins from Fusarium graminearum and related species.

J Basic Microbiol 2012 Apr 21;52(2):184-94. Epub 2011 Jul 21.

VTT Technical Research Centre of Finland, Helsinki, Finland.

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http://dx.doi.org/10.1002/jobm.201100053DOI Listing
April 2012

Counting absolute numbers of molecules using unique molecular identifiers.

Nat Methods 2011 Nov 20;9(1):72-4. Epub 2011 Nov 20.

Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1038/nmeth.1778DOI Listing
November 2011

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

EMBO J 2010 Jul 1;29(13):2147-60. Epub 2010 Jun 1.

Public Health Genomics Unit, National Institute for Health and Welfare (THL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland.

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http://dx.doi.org/10.1038/emboj.2010.106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905244PMC
July 2010

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

Genome Res 2010 Jun 8;20(6):861-73. Epub 2010 Apr 8.

Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland.

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http://dx.doi.org/10.1101/gr.100552.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582PMC
June 2010

Dynamic covariation between gene expression and genome characteristics.

Gene 2008 Feb 8;410(1):53-66. Epub 2007 Dec 8.

Institute of Medical Technology, University of Tampere, Finland.

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http://dx.doi.org/10.1016/j.gene.2007.11.018DOI Listing
February 2008

Optimization of cDNA-AFLP experiments using genomic sequence data.

Bioinformatics 2005 Jun 17;21(11):2573-9. Epub 2005 Mar 17.

Department of Computer Science, University of Helsinki, Helsinki, PO Box 68, FIN-00014, Finland.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti393DOI Listing
June 2005

Data integration and visualization system for enabling conceptual biology.

Bioinformatics 2005 Jun;21 Suppl 1:i177-85

VTT Biotechnology PO Box 1500, Espoo, FIN-02044 VTT, Finland.

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http://dx.doi.org/10.1093/bioinformatics/bti1015DOI Listing
June 2005

Assigning probes into a small number of pools separable by electrophoresis.

Bioinformatics 2002 ;18 Suppl 1:S199-206

Department of Computer Science, University of Helsinki, Teollisuuskatu 23, Helsinki, PO Box 26, FIN-00014, Finland.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s199DOI Listing
October 2004