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Items: 1 to 50 of 105

1.

CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J.

Nat Med. 2018 Jun 11. doi: 10.1038/s41591-018-0049-z. [Epub ahead of print]

PMID:
29892067
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.

Informational limits of biological organisms.

Taipale J.

EMBO J. 2018 May 15;37(10). pii: e96114. doi: 10.15252/embj.201696114. Epub 2018 Apr 18. No abstract available.

PMID:
29669861
4.

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.

5.

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.

PMID:
29425488
6.

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.

7.

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.

8.

Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer.

Kondelin J, Gylfe AE, Lundgren S, Tanskanen T, Hamberg J, Aavikko M, Palin K, Ristolainen H, Katainen R, Kaasinen E, Taipale M, Taipale J, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Vahteristo P, Tuupanen S, Aaltonen LA, Pitkänen E.

Cancer Res. 2017 Aug 1;77(15):4078-4088. doi: 10.1158/0008-5472.CAN-17-0682. Epub 2017 Jun 13.

PMID:
28611049
9.

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth.

Dave K, Sur I, Yan J, Zhang J, Kaasinen E, Zhong F, Blaas L, Li X, Kharazi S, Gustafsson C, De Paepe A, Månsson R, Taipale J.

Elife. 2017 Jun 6;6. pii: e23382. doi: 10.7554/eLife.23382.

10.

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
11.

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
12.

Structural perspective of cooperative transcription factor binding.

Morgunova E, Taipale J.

Curr Opin Struct Biol. 2017 Dec;47:1-8. doi: 10.1016/j.sbi.2017.03.006. Epub 2017 Mar 24. Review.

13.

The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression.

Liu NQ, Ter Huurne M, Nguyen LN, Peng T, Wang SY, Studd JB, Joshi O, Ongen H, Bramsen JB, Yan J, Andersen CL, Taipale J, Dermitzakis ET, Houlston RS, Hubner NC, Stunnenberg HG.

Nat Commun. 2017 Feb 14;8:14418. doi: 10.1038/ncomms14418.

14.

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.

15.

Damaging heterozygous mutations in NFKB1 lead to diverse immunologic phenotypes.

Kaustio M, Haapaniemi E, Göös H, Hautala T, Park G, Syrjänen J, Einarsdottir E, Sahu B, Kilpinen S, Rounioja S, Fogarty CL, Glumoff V, Kulmala P, Katayama S, Tamene F, Trotta L, Morgunova E, Krjutškov K, Nurmi K, Eklund K, Lagerstedt A, Helminen M, Martelius T, Mustjoki S, Taipale J, Saarela J, Kere J, Varjosalo M, Seppänen M.

J Allergy Clin Immunol. 2017 Sep;140(3):782-796. doi: 10.1016/j.jaci.2016.10.054. Epub 2017 Jan 21.

PMID:
28115215
16.

Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry.

Heikkinen T, Kämpjärvi K, Keskitalo S, von Nandelstadh P, Liu X, Rantanen V, Pitkänen E, Kinnunen M, Kuusanmäki H, Kontro M, Turunen M, Mäkinen N, Taipale J, Heckman C, Lehti K, Mustjoki S, Varjosalo M, Vahteristo P.

Hum Mutat. 2017 Mar;38(3):269-274. doi: 10.1002/humu.23157. Epub 2017 Jan 11.

PMID:
28054750
17.

Fast motif matching revisited: high-order PWMs, SNPs and indels.

Korhonen JH, Palin K, Taipale J, Ukkonen E.

Bioinformatics. 2017 Feb 15;33(4):514-521. doi: 10.1093/bioinformatics/btw683.

PMID:
28011774
18.

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.

19.

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.

20.

Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease.

Orlando G, Law PJ, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Kaprio J, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Mecklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Tenesa A, Farrington S, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Taipale J, Cheadle JP, Dunlop MG, Tomlinson IP, Aaltonen LA, Houlston RS.

Hum Mol Genet. 2016 Jun 1;25(11):2349-2359. Epub 2016 Mar 22.

21.

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
22.

Self-regulation and Beyond: Affect Regulation and the Infant-Caregiver Dyad.

Taipale J.

Front Psychol. 2016 Jun 15;7:889. doi: 10.3389/fpsyg.2016.00889. eCollection 2016.

23.

The role of enhancers in cancer.

Sur I, Taipale J.

Nat Rev Cancer. 2016 Aug;16(8):483-93. doi: 10.1038/nrc.2016.62. Epub 2016 Jul 1. Review.

PMID:
27364481
24.

Mendelian randomisation analysis strongly implicates adiposity with risk of developing colorectal cancer.

Jarvis D, Mitchell JS, Law PJ, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J, Kaasinen E, Sarin AP, Kaprio J, Eriksson JG, Rissanen H, Knekt P, Pukkala E, Jousilahti P, Salomaa V, Ripatti S, Palotie A, Järvinen H, Renkonen-Sinisalo L, Lepistö A, Böhm J, Meklin JP, Al-Tassan NA, Palles C, Martin L, Barclay E, Farrington SM, Timofeeva MN, Meyer BF, Wakil SM, Campbell H, Smith CG, Idziaszczyk S, Maughan TS, Kaplan R, Kerr R, Kerr D, Buchanan DD, Win AK, Hopper JL, Jenkins MA, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Taipale J, Aaltonen LA, Cheadle JP, Dunlop MG, Tomlinson IP, Houlston RS.

Br J Cancer. 2016 Jul 12;115(2):266-72. doi: 10.1038/bjc.2016.188. Epub 2016 Jun 23.

25.

Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication.

Balistreri G, Viiliäinen J, Turunen M, Diaz R, Lyly L, Pekkonen P, Rantala J, Ojala K, Sarek G, Teesalu M, Denisova O, Peltonen K, Julkunen I, Varjosalo M, Kainov D, Kallioniemi O, Laiho M, Taipale J, Hautaniemi S, Ojala PM.

PLoS Pathog. 2016 Feb 18;12(2):e1005424. doi: 10.1371/journal.ppat.1005424. eCollection 2016 Feb.

26.

Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12.

Mäkinen N, Aavikko M, Heikkinen T, Taipale M, Taipale J, Koivisto-Korander R, Bützow R, Vahteristo P.

PLoS Genet. 2016 Feb 18;12(2):e1005850. doi: 10.1371/journal.pgen.1005850. eCollection 2016 Feb.

27.

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.

28.

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
29.

Somatic MED12 mutations in prostate cancer and uterine leiomyomas promote tumorigenesis through distinct mechanisms.

Kämpjärvi K, Kim NH, Keskitalo S, Clark AD, von Nandelstadh P, Turunen M, Heikkinen T, Park MJ, Mäkinen N, Kivinummi K, Lintula S, Hotakainen K, Nevanlinna H, Hokland P, Böhling T, Bützow R, Böhm J, Mecklin JP, Järvinen H, Kontro M, Visakorpi T, Taipale J, Varjosalo M, Boyer TG, Vahteristo P.

Prostate. 2016 Jan;76(1):22-31. doi: 10.1002/pros.23092. Epub 2015 Sep 18.

PMID:
26383637
30.

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
31.

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.

32.

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, Whiffin N, Carnicer MJ, Broome L, Dryden N, Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O, Houlston RS.

Nat Commun. 2015 Feb 19;6:6178. doi: 10.1038/ncomms7178.

33.

Cancer. Cancer by super-enhancer.

Vähärautio A, Taipale J.

Science. 2014 Dec 12;346(6215):1291-2. doi: 10.1126/science.aaa3247. No abstract available.

PMID:
25504702
34.

Identification of 33 candidate oncogenes by screening for base-specific mutations.

Tuupanen S, Hänninen UA, Kondelin J, von Nandelstadh P, Cajuso T, Gylfe AE, Katainen R, Tanskanen T, Ristolainen H, Böhm J, Mecklin JP, Järvinen H, Renkonen-Sinisalo L, Andersen CL, Taipale M, Taipale J, Vahteristo P, Lehti K, Pitkänen E, Aaltonen LA.

Br J Cancer. 2014 Oct 14;111(8):1657-62. doi: 10.1038/bjc.2014.429. Epub 2014 Aug 12.

35.

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.

36.

Mutation analysis of components of the Mediator kinase module in MED12 mutation-negative uterine leiomyomas.

Mäkinen N, Heinonen HR, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA.

Br J Cancer. 2014 Apr 29;110(9):2246-9. doi: 10.1038/bjc.2014.138. Epub 2014 Mar 18.

37.

Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer.

Pitkänen E, Cajuso T, Katainen R, Kaasinen E, Välimäki N, Palin K, Taipale J, Aaltonen LA, Kilpivaara O.

Oncotarget. 2014 Feb 15;5(3):853-9.

38.

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
39.

Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer.

Cajuso T, Hänninen UA, Kondelin J, Gylfe AE, Tanskanen T, Katainen R, Pitkänen E, Ristolainen H, Kaasinen E, Taipale M, Taipale J, Böhm J, Renkonen-Sinisalo L, Mecklin JP, Järvinen H, Tuupanen S, Kilpivaara O, Vahteristo P.

Int J Cancer. 2014 Aug 1;135(3):611-23. doi: 10.1002/ijc.28705. Epub 2014 Jan 13.

40.

Eleven candidate susceptibility genes for common familial colorectal cancer.

Gylfe AE, Katainen R, Kondelin J, Tanskanen T, Cajuso T, Hänninen U, Taipale J, Taipale M, Renkonen-Sinisalo L, Järvinen H, Mecklin JP, Kilpivaara O, Pitkänen E, Vahteristo P, Tuupanen S, Karhu A, Aaltonen LA.

PLoS Genet. 2013;9(10):e1003876. doi: 10.1371/journal.pgen.1003876. Epub 2013 Oct 17.

41.

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.

42.

Lessons from functional analysis of genome-wide association studies.

Sur I, Tuupanen S, Whitington T, Aaltonen LA, Taipale J.

Cancer Res. 2013 Jul 15;73(14):4180-4. doi: 10.1158/0008-5472.CAN-13-0789. Epub 2013 Jul 5. Review.

43.

Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.

Gylfe AE, Kondelin J, Turunen M, Ristolainen H, Katainen R, Pitkänen E, Kaasinen E, Rantanen V, Tanskanen T, Varjosalo M, Lehtonen H, Palin K, Taipale M, Taipale J, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Ristimäki A, Kilpivaara O, Tuupanen S, Karhu A, Vahteristo P, Aaltonen LA.

Gastroenterology. 2013 Sep;145(3):540-3.e22. doi: 10.1053/j.gastro.2013.05.015. Epub 2013 May 16.

PMID:
23684749
44.

A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila.

Bischof J, Björklund M, Furger E, Schertel C, Taipale J, Basler K.

Development. 2013 Jun;140(11):2434-42. doi: 10.1242/dev.088757. Epub 2013 May 1.

45.

Systematic screening of a Drosophila ORF library in vivo uncovers Wnt/Wg pathway components.

Schertel C, Huang D, Björklund M, Bischof J, Yin D, Li R, Wu Y, Zeng R, Wu J, Taipale J, Song H, Basler K.

Dev Cell. 2013 Apr 29;25(2):207-19. doi: 10.1016/j.devcel.2013.02.019. Epub 2013 Apr 11.

46.

Human kinome analysis reveals novel kinases contributing to virus infection and retinoic-acid inducible gene I-induced type I and type III IFN gene expression.

Nousiainen L, Sillanpää M, Jiang M, Thompson J, Taipale J, Julkunen I.

Innate Immun. 2013 Oct;19(5):516-30. doi: 10.1177/1753425912473345. Epub 2013 Feb 12.

PMID:
23405030
47.

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.

48.

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.

49.

Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors.

Sur IK, Hallikas O, Vähärautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J.

Science. 2012 Dec 7;338(6112):1360-3. doi: 10.1126/science.1228606. Epub 2012 Nov 1.

50.

Loss of SUFU function in familial multiple meningioma.

Aavikko M, Li SP, Saarinen S, Alhopuro P, Kaasinen E, Morgunova E, Li Y, Vesanen K, Smith MJ, Evans DG, Pöyhönen M, Kiuru A, Auvinen A, Aaltonen LA, Taipale J, Vahteristo P.

Am J Hum Genet. 2012 Sep 7;91(3):520-6. doi: 10.1016/j.ajhg.2012.07.015.

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