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Items: 1 to 50 of 134

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 Sep;10(9). pii: e8552. doi: 10.15252/emmm.201708552.

2.

Glycomic Profiling Highlights Increased Fucosylation in Pseudomyxoma Peritonei.

Saarinen L, Nummela P, Leinonen H, Heiskanen A, Thiel A, Haglund C, Lepistö A, Satomaa T, Hautaniemi S, Ristimäki A.

Mol Cell Proteomics. 2018 Aug 2. pii: mcp.RA118.000615. doi: 10.1074/mcp.RA118.000615. [Epub ahead of print]

3.

PROX1 is a transcriptional regulator of MMP14.

Gramolelli S, Cheng J, Martinez-Corral I, Vähä-Koskela M, Elbasani E, Kaivanto E, Rantanen V, Tuohinto K, Hautaniemi S, Bower M, Haglund C, Alitalo K, Mäkinen T, Petrova TV, Lehti K, Ojala PM.

Sci Rep. 2018 Jun 22;8(1):9531. doi: 10.1038/s41598-018-27739-w.

4.

Identifying differentially methylated sites in samples with varying tumor purity.

Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S.

Bioinformatics. 2018 Sep 15;34(18):3078-3085. doi: 10.1093/bioinformatics/bty310.

PMID:
29912358
5.

A Functional Homologous Recombination Assay Predicts Primary Chemotherapy Response and Long-Term Survival in Ovarian Cancer Patients.

Tumiati M, Hietanen S, Hynninen J, Pietilä E, Färkkilä A, Kaipio K, Roering P, Huhtinen K, Alkodsi A, Li Y, Lehtonen R, Erkan EP, Tuominen MM, Lehti K, Hautaniemi SK, Vähärautio A, Grénman S, Carpén O, Kauppi L.

Clin Cancer Res. 2018 Sep 15;24(18):4482-4493. doi: 10.1158/1078-0432.CCR-17-3770. Epub 2018 Jun 1.

PMID:
29858219
6.

Mathematical Modeling Predicts Response to Chemotherapy and Drug Combinations in Ovarian Cancer.

Kozłowska E, Färkkilä A, Vallius T, Carpén O, Kemppainen J, Grénman S, Lehtonen R, Hynninen J, Hietanen S, Hautaniemi S.

Cancer Res. 2018 Jul 15;78(14):4036-4044. doi: 10.1158/0008-5472.CAN-17-3746. Epub 2018 May 16.

PMID:
29769198
7.

Clinical Value of 18F-fluorodeoxyglucose Positron Emission Tomography/Computed Tomography in Response Evaluation after Primary Treatment of Advanced Epithelial Ovarian Cancer.

Hynninen J, Laasik M, Vallius T, Kemppainen J, Grönroos S, Virtanen J, Casado J, Hautaniemi S, Grenman S, Seppänen M, Auranen A.

Clin Oncol (R Coll Radiol). 2018 Aug;30(8):507-514. doi: 10.1016/j.clon.2018.04.007. Epub 2018 May 9.

PMID:
29753662
8.

Lymphatic endothelium stimulates melanoma metastasis and invasion via MMP14-dependent Notch3 and β1-integrin activation.

Pekkonen P, Alve S, Balistreri G, Gramolelli S, Tatti-Bugaeva O, Paatero I, Niiranen O, Tuohinto K, Perälä N, Taiwo A, Zinovkina N, Repo P, Icay K, Ivaska J, Saharinen P, Hautaniemi S, Lehti K, Ojala PM.

Elife. 2018 May 1;7. pii: e32490. doi: 10.7554/eLife.32490.

9.

Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes.

Ullah I, Karthik GM, Alkodsi A, Kjällquist U, Stålhammar G, Lövrot J, Martinez NF, Lagergren J, Hautaniemi S, Hartman J, Bergh J.

J Clin Invest. 2018 Apr 2;128(4):1355-1370. doi: 10.1172/JCI96149. Epub 2018 Feb 26.

10.

Let-7 microRNA controls invasion-promoting lysosomal changes via the oncogenic transcription factor myeloid zinc finger-1.

Tvingsholm SA, Hansen MB, Clemmensen KKB, Brix DM, Rafn B, Frankel LB, Louhimo R, Moreira J, Hautaniemi S, Gromova I, Jäättelä M, Kallunki T.

Oncogenesis. 2018 Feb 3;7(2):14. doi: 10.1038/s41389-017-0014-6.

11.

MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B-cell lymphoma.

Leivonen SK, Icay K, Jäntti K, Siren I, Liu C, Alkodsi A, Cervera A, Ludvigsen M, Hamilton-Dutoit SJ, d'Amore F, Karjalainen-Lindsberg ML, Delabie J, Holte H, Lehtonen R, Hautaniemi S, Leppä S.

Blood Cancer J. 2017 Dec 15;7(12):654. doi: 10.1038/s41408-017-0033-8.

12.

Dynamic visualization of multi-level molecular data: The Director package in R.

Icay K, Liu C, Hautaniemi S.

Comput Methods Programs Biomed. 2018 Jan;153:129-136. doi: 10.1016/j.cmpb.2017.10.013. Epub 2017 Oct 12.

PMID:
29157446
13.

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma.

Leivonen SK, Taskinen M, Cervera A, Karjalainen-Lindsberg ML, Delabie J, Holte H, Lehtonen R, Hautaniemi S, Leppä S.

Blood Cancer J. 2017 Aug 25;7(8):e596. doi: 10.1038/bcj.2017.71.

14.

Multiple components of PKA and TGF-β pathways are mutated in pseudomyxoma peritonei.

Saarinen L, Nummela P, Thiel A, Lehtonen R, Järvinen P, Järvinen H, Aaltonen LA, Lepistö A, Hautaniemi S, Ristimäki A.

PLoS One. 2017 Apr 20;12(4):e0174898. doi: 10.1371/journal.pone.0174898. eCollection 2017.

15.

PerPAS: Topology-Based Single Sample Pathway Analysis Method.

Liu C, Lehtonen R, Hautaniemi S.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May-Jun;15(3):1022-1027. doi: 10.1109/TCBB.2017.2679745. Epub 2017 Mar 8.

PMID:
28287981
16.

Deltex-1 mutations predict poor survival in diffuse large B-cell lymphoma.

Meriranta L, Pasanen A, Louhimo R, Cervera A, Alkodsi A, Autio M, Taskinen M, Rantanen V, Karjalainen-Lindsberg ML, Holte H, Delabie J, Lehtonen R, Hautaniemi S, Leppä S.

Haematologica. 2017 May;102(5):e195-e198. doi: 10.3324/haematol.2016.157495. Epub 2017 Feb 9. No abstract available.

17.

DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival.

Fleischer T, Klajic J, Aure MR, Louhimo R, Pladsen AV, Ottestad L, Touleimat N, Laakso M, Halvorsen AR, Grenaker Alnæs GI, Riis ML, Helland Å, Hautaniemi S, Lønning PE, Naume B, Børresen-Dale AL, Tost J, Kristensen VN.

Oncotarget. 2017 Jan 3;8(1):1074-1082. doi: 10.18632/oncotarget.13718.

18.

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

Vassilev B, Louhimo R, Ikonen E, Hautaniemi S.

PLoS One. 2016 Oct 6;11(10):e0164023. doi: 10.1371/journal.pone.0164023. eCollection 2016.

19.

Complete androgen insensitivity syndrome caused by a deep intronic pseudoexon-activating mutation in the androgen receptor gene.

Känsäkoski J, Jääskeläinen J, Jääskeläinen T, Tommiska J, Saarinen L, Lehtonen R, Hautaniemi S, Frilander MJ, Palvimo JJ, Toppari J, Raivio T.

Sci Rep. 2016 Sep 9;6:32819. doi: 10.1038/srep32819.

20.

Data integration to prioritize drugs using genomics and curated data.

Louhimo R, Laakso M, Belitskin D, Klefström J, Lehtonen R, Hautaniemi S.

BioData Min. 2016 May 26;9:21. doi: 10.1186/s13040-016-0097-1. eCollection 2016.

21.

SePIA: RNA and small RNA sequence processing, integration, and analysis.

Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.

BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z. eCollection 2016.

22.

Novel Mad2-targeting miR-493-3p controls mitotic fidelity and cancer cells' sensitivity to paclitaxel.

Tambe M, Pruikkonen S, Mäki-Jouppila J, Chen P, Elgaaen BV, Straume AH, Huhtinen K, Cárpen O, Lønning PE, Davidson B, Hautaniemi S, Kallio MJ.

Oncotarget. 2016 Mar 15;7(11):12267-85. doi: 10.18632/oncotarget.7860.

23.

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.

24.

Transmembrane prostatic acid phosphatase (TMPAP) delays cells in G1 phase of the cell cycle.

Araujo CL, Quintero IB, Ovaska K, Herrala AM, Hautaniemi S, Vihko PT.

Prostate. 2016 Feb;76(2):151-62. doi: 10.1002/pros.23105. Epub 2015 Sep 30.

PMID:
26419820
25.

Prognostic value of tumour budding in oesophageal cancer: a meta-analysis.

Almangush A, Karhunen M, Hautaniemi S, Salo T, Leivo I.

Histopathology. 2016 Jan;68(2):173-82. doi: 10.1111/his.12781. Epub 2015 Sep 3. Review.

PMID:
26183253
26.

Identification of Prognostic Groups in High-Grade Serous Ovarian Cancer Treated with Platinum-Taxane Chemotherapy.

Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grénman S, Lehtonen R, Carpén O, Hautaniemi S.

Cancer Res. 2015 Aug 1;75(15):2987-98. doi: 10.1158/0008-5472.CAN-14-3242. Epub 2015 Jun 29.

27.

Par6G suppresses cell proliferation and is targeted by loss-of-function mutations in multiple cancers.

Marques E, Englund JI, Tervonen TA, Virkunen E, Laakso M, Myllynen M, Mäkelä A, Ahvenainen M, Lepikhova T, Monni O, Hautaniemi S, Klefström J.

Oncogene. 2016 Mar 17;35(11):1386-98. doi: 10.1038/onc.2015.196. Epub 2015 Jun 15.

28.

Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer.

Heinonen H, Lepikhova T, Sahu B, Pehkonen H, Pihlajamaa P, Louhimo R, Gao P, Wei GH, Hautaniemi S, Jänne OA, Monni O.

Int J Cancer. 2015 Nov 15;137(10):2374-83. doi: 10.1002/ijc.29616. Epub 2015 Jun 17.

29.

Early maternal alcohol consumption alters hippocampal DNA methylation, gene expression and volume in a mouse model.

Marjonen H, Sierra A, Nyman A, Rogojin V, Gröhn O, Linden AM, Hautaniemi S, Kaminen-Ahola N.

PLoS One. 2015 May 13;10(5):e0124931. doi: 10.1371/journal.pone.0124931. eCollection 2015.

30.

Identification of sample-specific regulations using integrative network level analysis.

Liu C, Louhimo R, Laakso M, Lehtonen R, Hautaniemi S.

BMC Cancer. 2015 Apr 28;15:319. doi: 10.1186/s12885-015-1265-2.

31.

MMP16 Mediates a Proteolytic Switch to Promote Cell-Cell Adhesion, Collagen Alignment, and Lymphatic Invasion in Melanoma.

Tatti O, Gucciardo E, Pekkonen P, Holopainen T, Louhimo R, Repo P, Maliniemi P, Lohi J, Rantanen V, Hautaniemi S, Alitalo K, Ranki A, Ojala PM, Keski-Oja J, Lehti K.

Cancer Res. 2015 May 15;75(10):2083-94. doi: 10.1158/0008-5472.CAN-14-1923. Epub 2015 Mar 25.

32.

Origins and impacts of new mammalian exons.

Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB.

Cell Rep. 2015 Mar 31;10(12):1992-2005. doi: 10.1016/j.celrep.2015.02.058. Epub 2015 Mar 19.

33.

Genomic profile of pseudomyxoma peritonei analyzed using next-generation sequencing and immunohistochemistry.

Nummela P, Saarinen L, Thiel A, Järvinen P, Lehtonen R, Lepistö A, Järvinen H, Aaltonen LA, Hautaniemi S, Ristimäki A.

Int J Cancer. 2015 Mar 1;136(5):E282-9. doi: 10.1002/ijc.29245. Epub 2014 Oct 13.

34.

Workflow for automated quantification of cerebromicrovascular gelatinase activity.

Mattila OS, Rantanen V, Saksi J, Strbian D, Pikkarainen T, Hautaniemi S, Lindsberg PJ.

Microvasc Res. 2015 Jan;97:19-24. doi: 10.1016/j.mvr.2014.08.009. Epub 2014 Sep 19.

PMID:
25242681
35.

Anima: modular workflow system for comprehensive image data analysis.

Rantanen V, Valori M, Hautaniemi S.

Front Bioeng Biotechnol. 2014 Jul 30;2:25. doi: 10.3389/fbioe.2014.00025. eCollection 2014.

36.

Dectin-1 pathway activates robust autophagy-dependent unconventional protein secretion in human macrophages.

Öhman T, Teirilä L, Lahesmaa-Korpinen AM, Cypryk W, Veckman V, Saijo S, Wolff H, Hautaniemi S, Nyman TA, Matikainen S.

J Immunol. 2014 Jun 15;192(12):5952-62. doi: 10.4049/jimmunol.1303213. Epub 2014 May 7.

37.

Prostatic acid phosphatase is the main acid phosphatase with 5'-ectonucleotidase activity in the male mouse saliva and regulates salivation.

Araujo CL, Quintero IB, Kipar A, Herrala AM, Pulkka AE, Saarinen L, Hautaniemi S, Vihko P.

Am J Physiol Cell Physiol. 2014 Jun 1;306(11):C1017-27. doi: 10.1152/ajpcell.00062.2014. Epub 2014 Apr 9.

38.

AIP inactivation leads to pituitary tumorigenesis through defective Gαi-cAMP signaling.

Tuominen I, Heliövaara E, Raitila A, Rautiainen MR, Mehine M, Katainen R, Donner I, Aittomäki V, Lehtonen HJ, Ahlsten M, Kivipelto L, Schalin-Jäntti C, Arola J, Hautaniemi S, Karhu A.

Oncogene. 2015 Feb 26;34(9):1174-84. doi: 10.1038/onc.2014.50. Epub 2014 Mar 24.

PMID:
24662816
39.

Biclustering methods: biological relevance and application in gene expression analysis.

Oghabian A, Kilpinen S, Hautaniemi S, Czeizler E.

PLoS One. 2014 Mar 20;9(3):e90801. doi: 10.1371/journal.pone.0090801. eCollection 2014.

40.

Deregulation of COMMD1 is associated with poor prognosis in diffuse large B-cell lymphoma.

Taskinen M, Louhimo R, Koivula S, Chen P, Rantanen V, Holte H, Delabie J, Karjalainen-Lindsberg ML, Björkholm M, Fluge Ø, Pedersen LM, Fjordén K, Jerkeman M, Eriksson M, Hautaniemi S, Leppä S.

PLoS One. 2014 Mar 13;9(3):e91031. doi: 10.1371/journal.pone.0091031. eCollection 2014.

41.

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data.

Alkodsi A, Louhimo R, Hautaniemi S.

Brief Bioinform. 2015 Mar;16(2):242-54. doi: 10.1093/bib/bbu004. Epub 2014 Mar 5.

PMID:
24599115
42.

Adipocyte morphology and implications for metabolic derangements in acquired obesity.

Heinonen S, Saarinen L, Naukkarinen J, Rodríguez A, Frühbeck G, Hakkarainen A, Lundbom J, Lundbom N, Vuolteenaho K, Moilanen E, Arner P, Hautaniemi S, Suomalainen A, Kaprio J, Rissanen A, Pietiläinen KH.

Int J Obes (Lond). 2014 Nov;38(11):1423-31. doi: 10.1038/ijo.2014.31. Epub 2014 Feb 19.

PMID:
24549139
43.

Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs.

Pihlajamaa P, Sahu B, Lyly L, Aittomäki V, Hautaniemi S, Jänne OA.

EMBO J. 2014 Feb 18;33(4):312-26. doi: 10.1002/embj.201385895. Epub 2014 Jan 22.

44.

Use of IgE and IgG4 epitope binding to predict the outcome of oral immunotherapy in cow's milk allergy.

Savilahti EM, Kuitunen M, Valori M, Rantanen V, Bardina L, Gimenez G, Mäkelä MJ, Hautaniemi S, Savilahti E, Sampson HA.

Pediatr Allergy Immunol. 2014 May;25(3):227-35. doi: 10.1111/pai.12186. Epub 2014 Jan 6.

45.

Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes.

Maliniemi P, Hahtola S, Ovaska K, Jeskanen L, Väkevä L, Jäntti K, Stadler R, Michonneau D, Fraitag S, Hautaniemi S, Ranki A.

Orphanet J Rare Dis. 2014 Nov 12;9:160. doi: 10.1186/s13023-014-0160-2.

46.

Identification of genetic markers with synergistic survival effect in cancer.

Louhimo R, Laakso M, Heikkinen T, Laitinen S, Manninen P, Rogojin V, Miettinen M, Blomqvist C, Liu J, Nevanlinna H, Hautaniemi S.

BMC Syst Biol. 2013;7 Suppl 1:S2. doi: 10.1186/1752-0509-7-S1-S2. Epub 2013 Aug 12.

47.

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.

Aure MR, Leivonen SK, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GI, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale AL, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN.

Genome Biol. 2013 Nov 20;14(11):R126. doi: 10.1186/gb-2013-14-11-r126.

48.

Characterising metabolically healthy obesity in weight-discordant monozygotic twins.

Naukkarinen J, Heinonen S, Hakkarainen A, Lundbom J, Vuolteenaho K, Saarinen L, Hautaniemi S, Rodriguez A, Frühbeck G, Pajunen P, Hyötyläinen T, Orešič M, Moilanen E, Suomalainen A, Lundbom N, Kaprio J, Rissanen A, Pietiläinen KH.

Diabetologia. 2014 Jan;57(1):167-76. doi: 10.1007/s00125-013-3066-y. Epub 2013 Oct 8.

PMID:
24100782
49.

Plasticity of blood- and lymphatic endothelial cells and marker identification.

Keuschnigg J, Karinen S, Auvinen K, Irjala H, Mpindi JP, Kallioniemi O, Hautaniemi S, Jalkanen S, Salmi M.

PLoS One. 2013 Sep 10;8(9):e74293. doi: 10.1371/journal.pone.0074293. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/cfda269a-cb46-4735-b87f-42afccb6aeb1.

50.

Transmembrane prostatic acid phosphatase (TMPAP) interacts with snapin and deficient mice develop prostate adenocarcinoma.

Quintero IB, Herrala AM, Araujo CL, Pulkka AE, Hautaniemi S, Ovaska K, Pryazhnikov E, Kulesskiy E, Ruuth MK, Soini Y, Sormunen RT, Khirug L, Vihko PT.

PLoS One. 2013 Sep 10;8(9):e73072. doi: 10.1371/journal.pone.0073072. eCollection 2013.

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