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Items: 1 to 50 of 63

1.

Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer.

Kondelin J, Salokas K, Saarinen L, Ovaska K, Rauanheimo H, Plaketti RM, Hamberg J, Liu X, Yadav L, Gylfe AE, Cajuso T, Hänninen UA, Palin K, Ristolainen H, Katainen R, Kaasinen E, Tanskanen T, Aavikko M, Taipale M, Taipale J, Renkonen-Sinisalo L, Lepistö A, Koskensalo S, Böhm J, Mecklin JP, Ongen H, Dermitzakis ET, Kilpivaara O, Vahteristo P, Turunen M, Hautaniemi S, Tuupanen S, Karhu A, Välimäki N, Varjosalo M, Pitkänen E, Aaltonen LA.

EMBO Mol Med. 2018 Aug 14. pii: e8552. doi: 10.15252/emmm.201708552. [Epub ahead of print]

2.

Two protein/protein interaction assays in one go.

Taipale M.

Mol Syst Biol. 2018 Jul 18;14(7):e8485. doi: 10.15252/msb.20188485. No abstract available.

3.

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
4.

Disruption of protein function by pathogenic mutations: common and uncommon mechanisms.

Taipale M.

Biochem Cell Biol. 2018 Apr 25. doi: 10.1139/bcb-2018-0007. [Epub ahead of print]

PMID:
29693415
5.

Exome-wide somatic mutation characterization of small bowel adenocarcinoma.

Hänninen UA, Katainen R, Tanskanen T, Plaketti RM, Laine R, Hamberg J, Ristimäki A, Pukkala E, Taipale M, Mecklin JP, Forsström LM, Pitkänen E, Palin K, Välimäki N, Mäkinen N, Aaltonen LA.

PLoS Genet. 2018 Mar 9;14(3):e1007200. doi: 10.1371/journal.pgen.1007200. eCollection 2018 Mar.

6.

Functional polymorphisms in asporin and CILP together with joint loading predispose to hand osteoarthritis.

Taipale M, Solovieva S, Leino-Arjas P, Männikkö M.

BMC Genet. 2017 Dec 12;18(1):108. doi: 10.1186/s12863-017-0585-4.

7.

Quantitative Profiling of Chaperone/Client Interactions with LUMIER Assay.

Taipale M.

Methods Mol Biol. 2018;1709:47-58. doi: 10.1007/978-1-4939-7477-1_4.

PMID:
29177650
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.

9.

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
10.

TUFT1, a novel candidate gene for metatarsophalangeal osteoarthritis, plays a role in chondrogenesis on a calcium-related pathway.

Sliz E, Taipale M, Welling M, Skarp S, Alaraudanjoki V, Ignatius J, Ruddock L, Nissi R, Männikkö M.

PLoS One. 2017 Apr 14;12(4):e0175474. doi: 10.1371/journal.pone.0175474. eCollection 2017.

11.

Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila.

Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska K, Nocek BP, Taipale M, Savchenko A, Ensminger AW.

Mol Syst Biol. 2016 Dec 16;12(12):893. doi: 10.15252/msb.20167381.

12.

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.

13.

Comparison of blood RNA isolation methods from samples stabilized in Tempus tubes and stored at a large human biobank.

Aarem J, Brunborg G, Aas KK, Harbak K, Taipale MM, Magnus P, Knudsen GP, Duale N.

BMC Res Notes. 2016 Sep 1;9(1):430. doi: 10.1186/s13104-016-2224-y.

14.

An inter-species protein-protein interaction network across vast evolutionary distance.

Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

15.

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.

16.

Targeted re-sequencing of linkage region on 2q21 identifies a novel functional variant for hip and knee osteoarthritis.

Taipale M, Jakkula E, Kämäräinen OP, Gao P, Skarp S, Barral S, Kiviranta I, Kröger H, Ott J, Wei GH, Ala-Kokko L, Männikkö M.

Osteoarthritis Cartilage. 2016 Apr;24(4):655-63. doi: 10.1016/j.joca.2015.10.019. Epub 2015 Nov 19.

17.

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
18.

Flight-induced changes in gene expression in the Glanville fritillary butterfly.

Kvist J, Mattila AL, Somervuo P, Ahola V, Koskinen P, Paulin L, Salmela L, Fountain T, Rastas P, Ruokolainen A, Taipale M, Holm L, Auvinen P, Lehtonen R, Frilander MJ, Hanski I.

Mol Ecol. 2015 Oct;24(19):4886-900. doi: 10.1111/mec.13359.

PMID:
26331775
19.

Widespread macromolecular interaction perturbations in human genetic disorders.

Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

20.

Systematic search for rare variants in Finnish early-onset colorectal cancer patients.

Tanskanen T, Gylfe AE, Katainen R, Taipale M, Renkonen-Sinisalo L, Järvinen H, Mecklin JP, Böhm J, Kilpivaara O, Pitkänen E, Palin K, Vahteristo P, Tuupanen S, Aaltonen LA.

Cancer Genet. 2015 Jan-Feb;208(1-2):35-40. doi: 10.1016/j.cancergen.2014.12.004. Epub 2014 Dec 31.

PMID:
25749350
21.

Whole-Genome Sequencing Identifies STAT4 as a Putative Susceptibility Gene in Classic Kaposi Sarcoma.

Aavikko M, Kaasinen E, Nieminen JK, Byun M, Donner I, Mancuso R, Ferrante P, Clerici M, Brambilla L, Tourlaki A, Sarid R, Guttman-Yassky E, Taipale M, Morgunova E, Pekkonen P, Ojala PM, Pukkala E, Casanova JL, Vaarala O, Vahteristo P, Aaltonen LA.

J Infect Dis. 2015 Jun 1;211(11):1842-51. doi: 10.1093/infdis/jiu667. Epub 2014 Dec 9.

PMID:
25492914
22.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I.

Nat Commun. 2014 Sep 5;5:4737. doi: 10.1038/ncomms5737.

23.

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.

24.

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.

Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S.

Cell. 2014 Jul 17;158(2):434-448. doi: 10.1016/j.cell.2014.05.039.

25.

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

Somervuo P, Kvist J, Ikonen S, Auvinen P, Paulin L, Koskinen P, Holm L, Taipale M, Duplouy A, Ruokolainen A, Saarnio S, Sirén J, Kohonen J, Corander J, Frilander MJ, Ahola V, Hanski I.

PLoS One. 2014 Jul 2;9(7):e101467. doi: 10.1371/journal.pone.0101467. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e104668.

26.

Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins.

DeBartolo J, Taipale M, Keating AE.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003693. doi: 10.1371/journal.pcbi.1003693. eCollection 2014 Jun.

27.

The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells.

Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I.

Nat Methods. 2014 May;11(5):585-92. doi: 10.1038/nmeth.2895. Epub 2014 Mar 23.

PMID:
24658140
28.

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.

29.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.

Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC.

Nat Methods. 2013 Dec;10(12):1239-45. doi: 10.1038/nmeth.2702. Epub 2013 Oct 27.

30.

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.

31.

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.

32.

Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells.

Taipale M, Krykbaeva I, Whitesell L, Santagata S, Zhang J, Liu Q, Gray NS, Lindquist S.

Nat Biotechnol. 2013 Jul;31(7):630-7. doi: 10.1038/nbt.2620. Epub 2013 Jun 30.

33.

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
34.

Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.

Tanskanen T, Gylfe AE, Katainen R, Taipale M, Renkonen-Sinisalo L, Mecklin JP, Järvinen H, Tuupanen S, Kilpivaara O, Vahteristo P, Aaltonen LA.

Scand J Gastroenterol. 2013 Jun;48(6):672-8. doi: 10.3109/00365521.2013.783102. Epub 2013 Apr 2.

PMID:
23544471
35.

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.

36.

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.

37.

Widespread regulation of translation by elongation pausing in heat shock.

Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB.

Mol Cell. 2013 Feb 7;49(3):439-52. doi: 10.1016/j.molcel.2012.11.028. Epub 2013 Jan 3.

38.

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.

39.

Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition.

Taipale M, Krykbaeva I, Koeva M, Kayatekin C, Westover KD, Karras GI, Lindquist S.

Cell. 2012 Aug 31;150(5):987-1001. doi: 10.1016/j.cell.2012.06.047.

40.

The aromatase gene CYP19A1: several genetic and functional lines of evidence supporting a role in reading, speech and language.

Anthoni H, Sucheston LE, Lewis BA, Tapia-Páez I, Fan X, Zucchelli M, Taipale M, Stein CM, Hokkanen ME, Castrén E, Pennington BF, Smith SD, Olson RK, Tomblin JB, Schulte-Körne G, Nöthen M, Schumacher J, Müller-Myhsok B, Hoffmann P, Gilger JW, Hynd GW, Nopola-Hemmi J, Leppanen PH, Lyytinen H, Schoumans J, Nordenskjöld M, Spencer J, Stanic D, Boon WC, Simpson E, Mäkelä S, Gustafsson JÅ, Peyrard-Janvid M, Iyengar S, Kere J.

Behav Genet. 2012 Jul;42(4):509-27. doi: 10.1007/s10519-012-9532-3. Epub 2012 Mar 17.

41.

MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.

Mäkinen N, Mehine M, Tolvanen J, Kaasinen E, Li Y, Lehtonen HJ, Gentile M, Yan J, Enge M, Taipale M, Aavikko M, Katainen R, Virolainen E, Böhling T, Koski TA, Launonen V, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA.

Science. 2011 Oct 14;334(6053):252-5. doi: 10.1126/science.1208930. Epub 2011 Aug 25.

42.

Chronic suppurative otitis media in children of Luanda, Angola.

Taipale A, Pelkonen T, Taipale M, Bernardino L, Peltola H, Pitkäranta A.

Acta Paediatr. 2011 Aug;100(8):e84-8. doi: 10.1111/j.1651-2227.2011.02192.x. Epub 2011 Apr 8.

PMID:
21477130
43.

Otorhinolaryngological findings and hearing in HIV-positive and HIV-negative children in a developing country.

Taipale A, Pelkonen T, Taipale M, Roine I, Bernardino L, Peltola H, Pitkäranta A.

Eur Arch Otorhinolaryngol. 2011 Oct;268(10):1527-32. doi: 10.1007/s00405-011-1579-x. Epub 2011 Mar 25.

PMID:
21437696
44.

Protein homeostasis and the phenotypic manifestation of genetic diversity: principles and mechanisms.

Jarosz DF, Taipale M, Lindquist S.

Annu Rev Genet. 2010;44:189-216. doi: 10.1146/annurev.genet.40.110405.090412. Review.

PMID:
21047258
45.

HSP90 at the hub of protein homeostasis: emerging mechanistic insights.

Taipale M, Jarosz DF, Lindquist S.

Nat Rev Mol Cell Biol. 2010 Jul;11(7):515-28. doi: 10.1038/nrm2918. Epub 2010 Jun 9. Review.

PMID:
20531426
46.

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.

47.

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.

48.

The histone acetyltransferase hMOF is frequently downregulated in primary breast carcinoma and medulloblastoma and constitutes a biomarker for clinical outcome in medulloblastoma.

Pfister S, Rea S, Taipale M, Mendrzyk F, Straub B, Ittrich C, Thuerigen O, Sinn HP, Akhtar A, Lichter P.

Int J Cancer. 2008 Mar 15;122(6):1207-13.

49.

Epigenetiikka, geeninsäätely ja syöpä.

Taipale M.

Duodecim. 2006;122(21):2611-8. Finnish. No abstract available.

PMID:
17233338
50.

Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila.

Mendjan S, Taipale M, Kind J, Holz H, Gebhardt P, Schelder M, Vermeulen M, Buscaino A, Duncan K, Mueller J, Wilm M, Stunnenberg HG, Saumweber H, Akhtar A.

Mol Cell. 2006 Mar 17;21(6):811-23.

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