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Items: 22

1.

The Human Transcription Factors.

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT.

Cell. 2018 Oct 4;175(2):598-599. doi: 10.1016/j.cell.2018.09.045. No abstract available.

2.

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
3.

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J.

Elife. 2018 Apr 11;7. pii: e32963. doi: 10.7554/eLife.32963.

4.

The Human Transcription Factors.

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT.

Cell. 2018 Feb 8;172(4):650-665. doi: 10.1016/j.cell.2018.01.029. Review. Erratum in: Cell. 2018 Oct 4;175(2):598-599.

5.

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.

6.

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
7.

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates.

Mall M, Kareta MS, Chanda S, Ahlenius H, Perotti N, Zhou B, Grieder SD, Ge X, Drake S, Euong Ang C, Walker BM, Vierbuchen T, Fuentes DR, Brennecke P, Nitta KR, Jolma A, Steinmetz LM, Taipale J, Südhof TC, Wernig M.

Nature. 2017 Apr 13;544(7649):245-249. doi: 10.1038/nature21722. Epub 2017 Apr 5.

PMID:
28379941
8.

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.

Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R.

Mol Syst Biol. 2017 Feb 6;13(2):910. doi: 10.15252/msb.20167238.

9.

Multiparameter functional diversity of human C2H2 zinc finger proteins.

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR.

Genome Res. 2016 Dec;26(12):1742-1752. Epub 2016 Nov 16.

10.

Structural insights into the DNA-binding specificity of E2F family transcription factors.

Morgunova E, Yin Y, Jolma A, Dave K, Schmierer B, Popov A, Eremina N, Nilsson L, Taipale J.

Nat Commun. 2015 Dec 3;6:10050. doi: 10.1038/ncomms10050.

11.

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
12.

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.

14.

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.

Huang Q, Whitington T, Gao P, Lindberg JF, Yang Y, Sun J, Väisänen MR, Szulkin R, Annala M, Yan J, Egevad LA, Zhang K, Lin R, Jolma A, Nykter M, Manninen A, Wiklund F, Vaarala MH, Visakorpi T, Xu J, Taipale J, Wei GH.

Nat Genet. 2014 Feb;46(2):126-35. doi: 10.1038/ng.2862. Epub 2014 Jan 5.

PMID:
24390282
15.

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.

16.

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.

17.

Beyond the balance of activator and repressor.

Whitington T, Jolma A, Taipale J.

Sci Signal. 2011 Jun 7;4(176):pe29. doi: 10.1126/scisignal.2002183.

PMID:
21653226
18.

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.

Jolma A, Taipale J.

Subcell Biochem. 2011;52:155-73. doi: 10.1007/978-90-481-9069-0_7. Review.

PMID:
21557082
19.

Combining conservation value, vulnerability, and effectiveness of mitigation actions in spatial conservation decisions: an application to coastal oil spill combating.

Ihaksi T, Kokkonen T, Helle I, Jolma A, Lecklin T, Kuikka S.

Environ Manage. 2011 May;47(5):802-13. doi: 10.1007/s00267-011-9639-y. Epub 2011 Mar 25.

PMID:
21437741
20.

Modeling the effectiveness of oil combating from an ecological perspective--a Bayesian network for the Gulf of Finland; the Baltic Sea.

Helle I, Lecklin T, Jolma A, Kuikka S.

J Hazard Mater. 2011 Jan 15;185(1):182-92. doi: 10.1016/j.jhazmat.2010.09.017. Epub 2010 Sep 17.

PMID:
20934249
21.

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.

22.

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.

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