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Items: 31

1.

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

Wei B, Jolma A, Sahu B, Orre LM, Zhong F, Zhu F, Kivioja T, Sur I, Lehtiö J, Taipale M, Taipale J.

Nat Biotechnol. 2018 Jul;36(6):521-529. doi: 10.1038/nbt.4138. Epub 2018 May 21.

PMID:
29786094
2.

NRF2, DJ1 and SNRX1 and their prognostic impact in astrocytic gliomas.

Haapasalo J, Nordfors K, Granberg KJ, Kivioja T, Nykter M, Haapasalo H, Soini Y.

Histol Histopathol. 2018 Feb 14:11973. doi: 10.14670/HH-11-973. [Epub ahead of print]

PMID:
29441509
3.

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.

Nucleic Acids Res. 2018 May 4;46(8):e44. doi: 10.1093/nar/gky027.

4.

CRISPR/Cas9 screening using unique molecular identifiers.

Schmierer B, Botla SK, Zhang J, Turunen M, Kivioja T, Taipale J.

Mol Syst Biol. 2017 Oct 9;13(10):945. doi: 10.15252/msb.20177834.

5.

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 PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J.

Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239.

PMID:
28473536
6.

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.

Cell Cycle. 2017 Jan 17;16(2):189-199. doi: 10.1080/15384101.2016.1261765. Epub 2016 Dec 8.

7.

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

Hartonen T, Sahu B, Dave K, Kivioja T, Taipale J.

Bioinformatics. 2016 Sep 1;32(17):i629-i638. doi: 10.1093/bioinformatics/btw448.

PMID:
27587683
8.

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

Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J.

Nature. 2015 Nov 19;527(7578):384-8. doi: 10.1038/nature15518. Epub 2015 Nov 9.

PMID:
26550823
9.

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

Katainen R, Dave K, Pitkänen E, Palin K, Kivioja T, Välimäki N, Gylfe AE, Ristolainen H, Hänninen UA, Cajuso T, Kondelin J, Tanskanen T, Mecklin JP, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Kaasinen E, Kilpivaara O, Tuupanen S, Enge M, Taipale J, Aaltonen LA.

Nat Genet. 2015 Jul;47(7):818-21. doi: 10.1038/ng.3335. Epub 2015 Jun 8.

PMID:
26053496
10.

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

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J.

Elife. 2015 Mar 17;4. doi: 10.7554/eLife.04837.

11.

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

Turunen M, Spaeth JM, Keskitalo S, Park MJ, Kivioja T, Clark AD, Mäkinen N, Gao F, Palin K, Nurkkala H, Vähärautio A, Aavikko M, Kämpjärvi K, Vahteristo P, Kim CA, Aaltonen LA, Varjosalo M, Taipale J, Boyer TG.

Cell Rep. 2014 May 8;7(3):654-60. doi: 10.1016/j.celrep.2014.03.047. Epub 2014 Apr 18.

12.

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.

Cell. 2013 Aug 15;154(4):801-13. doi: 10.1016/j.cell.2013.07.034.

13.

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

14.

Transcriptional networks controlling the cell cycle.

Bonke M, Turunen M, Sokolova M, Vähärautio A, Kivioja T, Taipale M, Björklund M, Taipale J.

G3 (Bethesda). 2013 Jan;3(1):75-90. doi: 10.1534/g3.112.004283. Epub 2013 Jan 1.

15.

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.

Cell Death Differ. 2012 Dec;19(12):1992-2002. doi: 10.1038/cdd.2012.89. Epub 2012 Jul 13.

16.

Counting absolute numbers of molecules using unique molecular identifiers.

Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J.

Nat Methods. 2011 Nov 20;9(1):72-4. doi: 10.1038/nmeth.1778.

PMID:
22101854
17.

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

Sarlin T, Kivioja T, Kalkkinen N, Linder MB, Nakari-Setälä T.

J Basic Microbiol. 2012 Apr;52(2):184-94. doi: 10.1002/jobm.201100053. Epub 2011 Jul 21.

PMID:
21780148
18.

Detecting novel genes with sparse arrays.

Arvas M, Haiminen N, Smit B, Rautio J, Vitikainen M, Wiebe M, Martinez D, Chee C, Kunkel J, Sanchez C, Nelson MA, Pakula T, Saloheimo M, Penttilä M, Kivioja T.

Gene. 2010 Nov 1;467(1-2):41-51. doi: 10.1016/j.gene.2010.07.009. Epub 2010 Aug 5.

19.

Mutations in the circadian gene CLOCK in colorectal cancer.

Alhopuro P, Björklund M, Sammalkorpi H, Turunen M, Tuupanen S, Biström M, Niittymäki I, Lehtonen HJ, Kivioja T, Launonen V, Saharinen J, Nousiainen K, Hautaniemi S, Nuorva K, Mecklin JP, Järvinen H, Orntoft T, Arango D, Lehtonen R, Karhu A, Taipale J, Aaltonen LA.

Mol Cancer Res. 2010 Jul;8(7):952-60. doi: 10.1158/1541-7786.MCR-10-0086. Epub 2010 Jun 15.

20.

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

Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J.

EMBO J. 2010 Jul 7;29(13):2147-60. doi: 10.1038/emboj.2010.106. Epub 2010 Jun 1.

21.

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 JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J.

Genome Res. 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109. Epub 2010 Apr 8.

22.

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 JP, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA.

Nat Genet. 2009 Aug;41(8):885-90. doi: 10.1038/ng.406. Epub 2009 Jun 28.

PMID:
19561604
23.

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 HG, He WW, Ojala P, Taipale J.

Cell. 2008 May 2;133(3):537-48. doi: 10.1016/j.cell.2008.02.047.

24.

Dynamic covariation between gene expression and genome characteristics.

Kivioja T, Tiirikka T, Siermala M, Vihinen M.

Gene. 2008 Feb 29;410(1):53-66. doi: 10.1016/j.gene.2007.11.018. Epub 2007 Dec 8.

PMID:
18191345
25.

The EUROclass trial: defining subgroups in common variable immunodeficiency.

Wehr C, Kivioja T, Schmitt C, Ferry B, Witte T, Eren E, Vlkova M, Hernandez M, Detkova D, Bos PR, Poerksen G, von Bernuth H, Baumann U, Goldacker S, Gutenberger S, Schlesier M, Bergeron-van der Cruyssen F, Le Garff M, Debré P, Jacobs R, Jones J, Bateman E, Litzman J, van Hagen PM, Plebani A, Schmidt RE, Thon V, Quinti I, Espanol T, Webster AD, Chapel H, Vihinen M, Oksenhendler E, Peter HH, Warnatz K.

Blood. 2008 Jan 1;111(1):77-85. Epub 2007 Sep 26.

26.

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

Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S.

BMC Genomics. 2007 Sep 17;8:325.

27.

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

Rautio JJ, Bailey M, Kivioja T, Söderlund H, Penttilä M, Saloheimo M.

BMC Biotechnol. 2007 May 30;7:28.

28.

Data integration and visualization system for enabling conceptual biology.

Gopalacharyulu PV, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmén J, Oresic M.

Bioinformatics. 2005 Jun;21 Suppl 1:i177-85.

PMID:
15961455
29.

Optimization of cDNA-AFLP experiments using genomic sequence data.

Kivioja T, Arvas M, Saloheimo M, Penttilä M, Ukkonen E.

Bioinformatics. 2005 Jun 1;21(11):2573-9. Epub 2005 Mar 17.

PMID:
15774551
30.

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

Kivioja T, Arvas M, Kataja K, Penttilä M, Söderlund H, Ukkonen E.

Bioinformatics. 2002;18 Suppl 1:S199-206.

PMID:
12169548
31.

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

Kivioja T, Ravantti J, Verkhovsky A, Ukkonen E, Bamford D.

J Struct Biol. 2000 Aug;131(2):126-34.

PMID:
11042083

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