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Items: 1 to 50 of 111

1.

Towards pan-genome read alignment to improve variation calling.

Valenzuela D, Norri T, Välimäki N, Pitkänen E, Mäkinen V.

BMC Genomics. 2018 May 9;19(Suppl 2):87. doi: 10.1186/s12864-018-4465-8.

2.

Germline alterations in a consecutive series of acute myeloid leukemia.

Wartiovaara-Kautto U, Hirvonen EAM, Pitkänen E, Heckman C, Saarela J, Kettunen K, Porkka K, Kilpivaara O.

Leukemia. 2018 Apr 10. doi: 10.1038/s41375-018-0049-5. [Epub ahead of print] No abstract available.

PMID:
29632341
3.

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.

4.

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing.

Pradhan B, Cajuso T, Katainen R, Sulo P, Tanskanen T, Kilpivaara O, Pitkänen E, Aaltonen LA, Kauppi L, Palin K.

Sci Rep. 2017 Nov 6;7(1):14521. doi: 10.1038/s41598-017-15076-3.

5.

Global metabolomic profiling of uterine leiomyomas.

Heinonen HR, Mehine M, Mäkinen N, Pasanen A, Pitkänen E, Karhu A, Sarvilinna NS, Sjöberg J, Heikinheimo O, Bützow R, Aaltonen LA, Kaasinen E.

Br J Cancer. 2017 Dec 5;117(12):1855-1864. doi: 10.1038/bjc.2017.361. Epub 2017 Oct 26.

PMID:
29073636
6.

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
7.

Multiple clinical characteristics separate MED12-mutation-positive and -negative uterine leiomyomas.

Heinonen HR, Pasanen A, Heikinheimo O, Tanskanen T, Palin K, Tolvanen J, Vahteristo P, Sjöberg J, Pitkänen E, Bützow R, Mäkinen N, Aaltonen LA.

Sci Rep. 2017 Apr 21;7(1):1015. doi: 10.1038/s41598-017-01199-0.

8.

Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera.

Hirvonen EAM, Pitkänen E, Hemminki K, Aaltonen LA, Kilpivaara O.

Hum Genomics. 2017 Apr 20;11(1):6. doi: 10.1186/s40246-017-0102-x.

9.

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
10.

Impact of AIP and inhibitory G protein alpha 2 proteins on clinical features of sporadic GH-secreting pituitary adenomas.

Ritvonen E, Pitkänen E, Karppinen A, Vehkavaara S, Demir H, Paetau A, Schalin-Jäntti C, Karhu A.

Eur J Endocrinol. 2017 Feb;176(2):243-252. doi: 10.1530/EJE-16-0620.

11.

Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction.

Castillo S, Barth D, Arvas M, Pakula TM, Pitkänen E, Blomberg P, Seppanen-Laakso T, Nygren H, Sivasiddarthan D, Penttilä M, Oja M.

Biotechnol Biofuels. 2016 Nov 21;9:252. eCollection 2016.

12.

MED12 mutations and FH inactivation are mutually exclusive in uterine leiomyomas.

Kämpjärvi K, Mäkinen N, Mehine M, Välipakka S, Uimari O, Pitkänen E, Heinonen HR, Heikkinen T, Tolvanen J, Ahtikoski A, Frizzell N, Sarvilinna N, Sjöberg J, Bützow R, Aaltonen LA, Vahteristo P.

Br J Cancer. 2016 Jun 14;114(12):1405-11. doi: 10.1038/bjc.2016.130. Epub 2016 May 17.

13.

Integrated data analysis reveals uterine leiomyoma subtypes with distinct driver pathways and biomarkers.

Mehine M, Kaasinen E, Heinonen HR, Mäkinen N, Kämpjärvi K, Sarvilinna N, Aavikko M, Vähärautio A, Pasanen A, Bützow R, Heikinheimo O, Sjöberg J, Pitkänen E, Vahteristo P, Aaltonen LA.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1315-20. doi: 10.1073/pnas.1518752113. Epub 2016 Jan 19.

14.

Whole-Genome Sequencing of Growth Hormone (GH)-Secreting Pituitary Adenomas.

Välimäki N, Demir H, Pitkänen E, Kaasinen E, Karppinen A, Kivipelto L, Schalin-Jäntti C, Aaltonen LA, Karhu A.

J Clin Endocrinol Metab. 2015 Oct;100(10):3918-27. doi: 10.1210/jc.2015-3129. Epub 2015 Aug 17.

PMID:
26280510
15.

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
16.

Clonally related uterine leiomyomas are common and display branched tumor evolution.

Mehine M, Heinonen HR, Sarvilinna N, Pitkänen E, Mäkinen N, Katainen R, Tuupanen S, Bützow R, Sjöberg J, Aaltonen LA.

Hum Mol Genet. 2015 Aug 1;24(15):4407-16. doi: 10.1093/hmg/ddv177. Epub 2015 May 10.

PMID:
25964426
17.

3'-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite unstable colorectal cancer with nearly perfect sensitivity.

Kondelin J, Tuupanen S, Gylfe AE, Aavikko M, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Andersen CL, Vahteristo P, Pitkänen E, Aaltonen LA.

Fam Cancer. 2015 Sep;14(3):449-53. doi: 10.1007/s10689-015-9804-1.

PMID:
25930744
18.

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
19.

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.

20.

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.

21.

MED12 mutation frequency in unselected sporadic uterine leiomyomas.

Heinonen HR, Sarvilinna NS, Sjöberg J, Kämpjärvi K, Pitkänen E, Vahteristo P, Mäkinen N, Aaltonen LA.

Fertil Steril. 2014 Oct;102(4):1137-42. doi: 10.1016/j.fertnstert.2014.06.040. Epub 2014 Aug 6.

PMID:
25108465
22.

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.

23.

Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttilä M, Rousu J, Arvas M.

PLoS Comput Biol. 2014 Feb 6;10(2):e1003465. doi: 10.1371/journal.pcbi.1003465. eCollection 2014 Feb.

24.

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.

25.

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.

26.

Characterization of uterine leiomyomas by whole-genome sequencing.

Mehine M, Kaasinen E, Mäkinen N, Katainen R, Kämpjärvi K, Pitkänen E, Heinonen HR, Bützow R, Kilpivaara O, Kuosmanen A, Ristolainen H, Gentile M, Sjöberg J, Vahteristo P, Aaltonen LA.

N Engl J Med. 2013 Jul 4;369(1):43-53. doi: 10.1056/NEJMoa1302736. Epub 2013 Jun 5.

27.

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
28.

Nationwide registry-based analysis of cancer clustering detects strong familial occurrence of Kaposi sarcoma.

Kaasinen E, Aavikko M, Vahteristo P, Patama T, Li Y, Saarinen S, Kilpivaara O, Pitkänen E, Knekt P, Laaksonen M, Artama M, Lehtonen R, Aaltonen LA, Pukkala E.

PLoS One. 2013;8(1):e55209. doi: 10.1371/journal.pone.0055209. Epub 2013 Jan 24.

29.

Computational methods for metabolic reconstruction.

Pitkänen E, Rousu J, Ukkonen E.

Curr Opin Biotechnol. 2010 Feb;21(1):70-7. doi: 10.1016/j.copbio.2010.01.010. Epub 2010 Feb 18.

PMID:
20171871
30.

13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose.

Jouhten P, Pitkänen E, Pakula T, Saloheimo M, Penttilä M, Maaheimo H.

BMC Syst Biol. 2009 Oct 29;3:104. doi: 10.1186/1752-0509-3-104.

31.

Inferring branching pathways in genome-scale metabolic networks.

Pitkänen E, Jouhten P, Rousu J.

BMC Syst Biol. 2009 Oct 29;3:103. doi: 10.1186/1752-0509-3-103.

32.

Towards structured output prediction of enzyme function.

Astikainen K, Holm L, Pitkänen E, Szedmak S, Rousu J.

BMC Proc. 2008 Dec 17;2 Suppl 4:S2.

33.

Filarioid nematodes in cattle, sheep and horses in Finland.

Solismaa M, Laaksonen S, Nylund M, Pitkänen E, Airakorpi R, Oksanen A.

Acta Vet Scand. 2008 Jun 16;50:20. doi: 10.1186/1751-0147-50-20.

34.

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Pitkänen E, Akerlund A, Rantanen A, Jouhten P, Ukkonen E.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-102.

PMID:
20134058
35.

Metabolic syndrome is associated with changes in D-mannose metabolism.

Pitkänen OM, Vanhanen H, Pitkänen E.

Scand J Clin Lab Invest. 1999 Dec;59(8):607-12.

PMID:
10691051
36.

Improvement of immunoglobulin M capture immunoassay specificity: toxoplasma antibody detection method as a model.

Tuuminen T, Seppänen H, Pitkänen EM, Palomäki P, Käpyaho K.

J Clin Microbiol. 1999 Jan;37(1):270-3.

37.

Enzymatic determination of unbound D-mannose in serum.

Pitkänen E, Pitkänen O, Uotila L.

Eur J Clin Chem Clin Biochem. 1997 Oct;35(10):761-6.

PMID:
9368794
39.

Proteinuria and plasma hexosugars in early-stage glomerulonephritis.

Pitkanen E.

Clin Nephrol. 1996 Apr;45(4):226-9.

PMID:
8861796
40.
41.

The involvement of fructose 2,6-bisphosphate in substrate cycle control in the nonoxidative stage of the pentose phosphate pathway. A phosphorus magnetic resonance spectroscopy study.

Belyaeva NF, Golubev MA, Grigorovich JA, Dubinsky ZV, Semenova NA, Pitkänen E, Korovkin BF.

Experientia. 1994 Aug 15;50(8):780-4.

PMID:
8070536
42.

Renal tubular reabsorption of 1,5-anhydro-D-glucitol and D-mannose in vivo in the rat.

Pitkänen E, Pitkänen OM.

Pflugers Arch. 1992 Mar;420(3-4):367-75.

PMID:
1598192
43.
44.

Plasma 1,5-anhydroglucitol in experimental galactosemia in the rat.

Pitkänen E, Pitkänen OM.

Experientia. 1990 Jan 15;46(1):85-7.

PMID:
2298285
45.

1,5-Anhydro-D-glucitol--a novel type of sugar in the human organism.

Pitkänen E.

Scand J Clin Lab Invest Suppl. 1990;201:55-62.

PMID:
2244184
46.

Correction of haemodialysis-associated anaemia by deferoxamine. Effects on serum aluminum and iron overload.

von Bonsdorff M, Sipilä R, Pitkänen E.

Scand J Urol Nephrol Suppl. 1990;131:49-54.

PMID:
2075470
47.

Evaluation of an immunoturbidimetric microalbuminuria assay.

Paloheimo L, Pajari-Backas M, Pitkänen E, Melamies L, Rissanen R.

J Clin Chem Clin Biochem. 1987 Dec;25(12):889-92.

PMID:
3127530
48.

Bioaerosols and office building ventilation systems.

Pitkänen E, Pellikka M, Kalliokoski P, Jantunen MJ.

Experientia Suppl. 1987;51:297-301.

PMID:
2958338
49.

Nephelometry of acute-phase glycoproteins by binding to concanavalin A.

Pitkänen EM, Palosuo T, Aho K, Putus-Tikkanen T, von Essen R.

Clin Chem. 1984 Nov;30(11):1834-5.

50.

Serum beta-N-acetylglucosaminidase and beta-glucuronidase activities in silicosis patients and in workers exposed to silica dust.

Koskinen H, Järvisalo J, Pitkänen E, Mutanen P, Zitting A.

Br J Dis Chest. 1984 Jul;78(3):217-24.

PMID:
6331485

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