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Items: 16

1.

Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy.

Lepikhova T, Karhemo PR, Louhimo R, Yadav B, Murumägi A, Kulesskiy E, Kivento M, Sihto H, Grénman R, Syrjänen SM, Kallioniemi O, Aittokallio T, Wennerberg K, Joensuu H, Monni O.

Mol Cancer Ther. 2018 Jul 3. pii: molcanther.0733.2017. doi: 10.1158/1535-7163.MCT-17-0733. [Epub ahead of print]

PMID:
29970484
2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

Comparative analysis of algorithms for integration of copy number and expression data.

Louhimo R, Lepikhova T, Monni O, Hautaniemi S.

Nat Methods. 2012 Feb 12;9(4):351-5. doi: 10.1038/nmeth.1893.

PMID:
22327835
15.

CNAmet: an R package for integrating copy number, methylation and expression data.

Louhimo R, Hautaniemi S.

Bioinformatics. 2011 Mar 15;27(6):887-8. doi: 10.1093/bioinformatics/btr019. Epub 2011 Jan 12.

PMID:
21228048
16.

Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme.

Ovaska K, Laakso M, Haapa-Paananen S, Louhimo R, Chen P, Aittomäki V, Valo E, Núñez-Fontarnau J, Rantanen V, Karinen S, Nousiainen K, Lahesmaa-Korpinen AM, Miettinen M, Saarinen L, Kohonen P, Wu J, Westermarck J, Hautaniemi S.

Genome Med. 2010 Sep 7;2(9):65. doi: 10.1186/gm186.

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