Teemu Kivioja

Publications

Research output per year 2000 2007 2010 2012 2013 2015 2017 2018 2020 2022 2022

• 32 Article
• 1 Conference article

Research output per year

Research output per year

Search results

• 2022

  A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites

  Pihlajamaa, P., Kauko, O., Sahu, B., Kivioja, T. & Taipale, J., 26 Sept 2022, In: Nature Biotechnology. 41, p. 197–203 26 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Sequence determinants of human gene regulatory elements

  Sahu, B., Hartonen, T., Pihlajamaa, P., Wei, B., Dave, K., Zhu, F., Kaasinen, E., Lidschreiber, K., Lidschreiber, M., Daub, C. O., Cramer, P., Kivioja, T. & Taipale, J., Mar 2022, In: Nature Genetics. 54, 3, p. 283-+ 35 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Upregulation of ribosome biogenesis via canonical E-boxes is required for Myc-driven proliferation

  Zielke, N., Vähärautio, A., Liu, J., Kivioja, T. & Taipale, J., 25 Apr 2022, In: Developmental Cell. 57, 8, p. 1024-+ 18 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2020

  A comparative genomics multitool for scientific discovery and conservation

  Zoonomia Consortium, Genereux, D. P., Serres, A., Armstrong, J., Kivioja, T., Taipale, J. & Karlsson, E. K., 12 Nov 2020, In: Nature. 587, 7833, p. 240-+ 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

  Jolma, A., Zhang, J., Mondragon, E., Morgunova, E., Kivioja, T., Laverty, K. U., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, T. R., Maher III, L. J. & Taipale, J., Jul 2020, In: Genome Research. 30, 7, p. 962-973 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2018

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

  Wei, B., Jolma, A., Sahu, B., Orre, L. M., Zhong, F., Zhu, F., Kivioja, T., Sur, I., Lehtiö, J., Taipale, M. & Taipale, J., Jun 2018, In: Nature Biotechnology. 36, 6, p. 521-+ 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Contribution of allelic imbalance to colorectal cancer

  Palin, K., Pitkänen, E., Turunen, M., Sahu, B., Pihlajamaa, P., Kivioja, T., Kaasinen, E., Välimäki, N., Hänninen, U. A., Cajuso, T., Aavikko, M., Tuupanen, S., Kilpivaara, O., van den Berg, L., Kondelin, J., Tanskanen, T., Katainen, R., Grau, M., Rauanheimo, H. & Plaketti, R.-M. & 20 others, Taira, A., Sulo, P., Hartonen, T., Dave, K., Schmierer, B., Botla, S., Sokolova, M., Vähärautio, A., Gladysz, K., Ongen, H., Dermitzakis, E., Bramsen, J. B., Orntoft, T. F., Andersen, C. L., Ristimäki, A., Lepistö, A., Renkonen-Sinisalo, L., Mecklin, J.-P., Taipale, J. & Aaltonen, L. A., 10 Sept 2018, In: Nature Communications. 9, 9 p., 3664.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

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

  Toivonen, J., Kivioja, T., Jolma, A., Yin, Y., Taipale, J. & Ukkonen, E., 4 May 2018, In: Nucleic Acids Research. 46, 8, 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2017

  CRISPR/Cas9 screening using unique molecular identifiers

  Schmierer, B., Botla, S. K., Zhang, J., Turunen, M., Kivioja, T. & Taipale, J., Oct 2017, In: Molecular Systems Biology. 13, 10, 8 p., 945.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion

  Sokolova, M., Turunen, M., Mortusewicz, O., Kivioja, T., Herr, P., Vähärautio, A., Björklund, M., Taipale, M., Helleday, T. & Taipale, J., 2017, In: Cell Cycle. 16, 2, p. 189-199 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

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

  Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., Nitta, K. R., Taipale, M., Popov, A., Ginno, P. A., Domcke, S., Yan, J., Schubeler, D., Vinson, C. & Taipale, J., 5 May 2017, In: Science. 356, 6337, p. 502-+ 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2016

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

  Hartonen, T., Sahu, B., Dave, K., Kivioja, T. & Taipale, J., 1 Sept 2016, In: Bioinformatics. 32, 17, p. 629-638 10 p.

  Research output: Contribution to journal › Conference article › Scientific › peer-review

  Open Access
• 2015

  Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

  Nitta, K. R., Jolma, A., Yin, Y., Morgunova, E., Kivioja, T., Akhtar, J., Hens, K., Toivonen, J., Deplancke, B., Furlong, E. E. M. & Taipale, J., 17 Mar 2015, In: eLife. 4, 20 p., 04837.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

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

  Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Valimaki, N., Gylfe, A. E., Ristolainen, H., Hanninen, U. A., Cajuso, T., Kondelin, J., Tanskanen, T., Mecklin, J.-P., Järvinen, H., Renkonen-Sinisalo, L., Lepisto, A., Kaasinen, E., Kilpivaara, O., Tuupanen, S. & Enge, M. & 2 others, Taipale, J. & Aaltonen, L. A., 1 Jul 2015, In: Nature Genetics. 47, 7, p. 818-+

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

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

  Jolma, A., Yin, Y., Nitta, K. R., Dave, K., Popov, A., Taipale, M., Enge, M., Kivioja, T., Morgunova, E. & Taipale, J., 19 Nov 2015, In: Nature. 527, 7578, p. 384-+ 18 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2014

  Uterine Leiomyoma-Linked MED12 Mutations Disrupt Mediator-Associated CDK Activity

  Turunen, M., Spaeth, J. M., Keskitalo, S., Park, M. J., Kivioja, T., Clark, A. D., Mäkinen, N., Gao, F., Palin, K., Nurkkala, H., Vaharautio, A., Aavikko, M., Kampjarvi, K., Vahteristo, P., Kim, C. A., Aaltonen, L. A., Varjosalo, M., Taipale, J. & Boyer, T. G., May 2014, In: Cell Reports. 7, 3, p. 654-660 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2013

  DNA-Binding Specificities of Human Transcription Factors

  Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P., Morgunova, E., Enge, M., Taipale, M. J. O., Wei, G., Palin, K., Vaquerizas, J. M., Vincentelli, R., Luscombe, N. M., Hughes, T. R., Lemaire, P., Ukkonen, E., Kivioja, T. & Taipale, J., 17 Jan 2013, In: Cell. 152, 1-2, p. 327-339 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Transcriptional Networks Controlling the Cell Cycle

  Bonke, M., Turunen, M., Sokolova, M., Vaharautio, A., Kivioja, T., Taipale, M., Björklund, M. & Taipale, J., Jan 2013, In: G3 - Genes genomes genetics. 3, 1, p. 75-90 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

  Yan, J., Enge, M., Whitington, T., Dave, K., Liu, J., Sur, I., Schmierer, B., Jolma, A., Kivioja, T., Taipale, M. & Taipale, J., 15 Aug 2013, In: Cell. 154, 4, p. 801-813 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2012

  Counting absolute numbers of molecules using unique molecular identifiers

  Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S. & Taipale, J., 2012, In: Nature methods. 9, 1, p. 72-74 3 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

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

  Sarlin, T., Kivioja, T., Kalkkinen, N., Linder, M. B. & Nakari-Setala, T., 2012, In: Journal of Basic Microbiology. 52, 2, p. 184-194 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• 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., 1 Dec 2012, In: Cell Death and Differentiation. 19, 12, p. 1992-2002 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2011

  Missing pattern discovery

  Angelov, S., Inenaga, S., Kivioja, T. & Mäkinen, V., 2011, In: Journal of Discrete Algorithms. 9, 2, p. 153-165 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2010

  Detecting novel genes with sparse arrays

  Arvas, M., Haiminen, N. S., Smit, B., Rautio, J., Vitikainen, M., Wiebe, M., Martinez, D., Chee, C., Kunkel, J., Sanchez, C., Nelson, M. A., Pakula, N., Saloheimo, M., Penttilä, M. & Kivioja, T., 2010, In: Gene. 467, 1-2, p. 41-51 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

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

  Wei, G.-H., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., Yan, J., Talukder, S., Turunen, M., Taipale, M., Stunnenberg, H. G., Ukkonen, E., Hughes, T. R., Bulyk, M. L. & Taipale, J., 2010, In: EMBO Journal. 29, 13, p. 2147-2160 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

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

  Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J. M., Yan, J., Sillanpää, M. J., Bonke, A. W. M., Palin, K., Talukder, S., Hughes, T. R., Luscombe, N. M., Ukkonen, E. & Taipale, J., 2010, In: Genome Research. 20, 6, p. 861-873 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Mutations in the Circadian Gene CLOCK in Colorectal Cancer

  Alhopuro, P., Björklund, M., Sammalkorpi, H. P., Turunen, M., Tuupanen, S. J., Bistrom, M., Niittymäki, I., Lehtonen, H., Kivioja, T., Launonen, V., Saharinen, J. M. N., Nousiainen, K. J., Hautaniemi, S., Nuorva, K., Mecklin, J.-P., Järvinen, H., Orntoft, T., Arango, D., Lehtonen, R. J. & Karhu, A. I. & 2 others, Taipale, J. & Aaltonen, L. A., 2010, In: Molecular Cancer Research. 8, 7, p. 952-960 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2009

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

  Tuupanen, S., Turunen, M., Lehtonen, R., Hallikas, O., Vanharanta, S., Kivioja, T., Björklund, M., Wei, G., Yan, J., Niittymäki, I., Mecklin, J.-P., Järvinen, H., Ristimäki, A., Di-Bernardo, M., East, P., Carvajal-Carmona, L., Houlston, R. S., Tomlinson, I., Palin, K. & Ukkonen, E. & 3 others, Karhu, A., Taipale, J. & Aaltonen, L. A., 2009, In: Nature Genetics. 41, 8, p. 885-890 6 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2008

  Application of active and kinase-deficient kinome collection for identification of kinases regulating hedgehog signaling

  Varjosalo, M., Björklund, M., Cheng, F., Syvänen, H., Kivioja, T., Kilpinen, S., Sun, Z., Kallioniemi, O., Stunnenberg, H. G., He, W.-W., Ojala, P. & Taipale, J., 2008, In: Cell. 133, 3, p. 537-548 12 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2007

  Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina

  Arvas, M., Kivioja, T., Mitchell, A., Saloheimo, M., Ussery, D., Penttilä, M. & Oliver, S., 2007, In: BMC Genomics. 8, p. 325 23 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis

  Rautio, J. J., Bailey, M., Kivioja, T., Söderlund, H., Penttilä, M. & Saloheimo, M., 2007, In: BMC Biotechnology. 7, 28, 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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• 2005

  Optimization of cDNA-AFLP experiments using genomic sequence data

  Kivioja, T., Arvas, M., Saloheimo, M., Penttilä, M. & Ukkonen, E., 2005, In: Bioinformatics. 21, 11, p. 2573-2579 7 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2000

  Local average intensity-based method for identifying spherical particles in electron micrographs

  Kivioja, T., Ravantti, J., Verkhovsky, A., Ukkonen, E. & Bamford, D., Aug 2000, In: Journal of Structural Biology. 131, 2, p. 126-134 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review