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Results: 1 to 20 of 45

1.

Group Factor Analysis.

Klami A, Virtanen S, Leppaaho E, Kaski S.

IEEE Trans Neural Netw Learn Syst. 2014 Dec 18. [Epub ahead of print]

PMID:
25532193
[PubMed - as supplied by publisher]
2.

Toward computational cumulative biology by combining models of biological datasets.

Faisal A, Peltonen J, Georgii E, Rung J, Kaski S.

PLoS One. 2014 Nov 26;9(11):e113053. doi: 10.1371/journal.pone.0113053. eCollection 2014.

PMID:
25427176
[PubMed - in process]
Free PMC Article
3.

Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis.

Khan SA, Virtanen S, Kallioniemi OP, Wennerberg K, Poso A, Kaski S.

Bioinformatics. 2014 Sep 1;30(17):i497-504. doi: 10.1093/bioinformatics/btu456.

PMID:
25161239
[PubMed - in process]
Free PMC Article
4.

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations.

Suvitaival T, Rogers S, Kaski S.

Bioinformatics. 2014 Sep 1;30(17):i461-7. doi: 10.1093/bioinformatics/btu455.

PMID:
25161234
[PubMed - in process]
Free PMC Article
5.

Integrative and personalized QSAR analysis in cancer by kernelized Bayesian matrix factorization.

Ammad-ud-din M, Georgii E, Gönen M, Laitinen T, Kallioniemi O, Wennerberg K, Poso A, Kaski S.

J Chem Inf Model. 2014 Aug 25;54(8):2347-59. doi: 10.1021/ci500152b. Epub 2014 Aug 6.

PMID:
25046554
[PubMed - in process]
6.

Stronger findings from mass spectral data through multi-peak modeling.

Suvitaival T, Rogers S, Kaski S.

BMC Bioinformatics. 2014 Jun 19;15:208. doi: 10.1186/1471-2105-15-208.

PMID:
24947013
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G; NCI DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

PMID:
24880487
[PubMed - in process]
8.

Exploration and retrieval of whole-metagenome sequencing samples.

Seth S, Välimäki N, Kaski S, Honkela A.

Bioinformatics. 2014 Sep 1;30(17):2471-9. doi: 10.1093/bioinformatics/btu340. Epub 2014 May 19.

PMID:
24845653
[PubMed - in process]
Free PMC Article
9.

Probabilistic drug connectivity mapping.

Parkkinen JA, Kaski S.

BMC Bioinformatics. 2014 Apr 17;15:113. doi: 10.1186/1471-2105-15-113.

PMID:
24742351
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression.

Marttinen P, Pirinen M, Sarin AP, Gillberg J, Kettunen J, Surakka I, Kangas AJ, Soininen P, O'Reilly P, Kaakinen M, Kähönen M, Lehtimäki T, Ala-Korpela M, Raitakari OT, Salomaa V, Järvelin MR, Ripatti S, Kaski S.

Bioinformatics. 2014 Jul 15;30(14):2026-34. doi: 10.1093/bioinformatics/btu140. Epub 2014 Mar 24.

PMID:
24665129
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome-wide association studies with high-dimensional phenotypes.

Marttinen P, Gillberg J, Havulinna A, Corander J, Kaski S.

Stat Appl Genet Mol Biol. 2013 Aug;12(4):413-31. doi: 10.1515/sagmb-2012-0032.

PMID:
23759510
[PubMed - indexed for MEDLINE]
12.

Targeted retrieval of gene expression measurements using regulatory models.

Georgii E, Salojärvi J, Brosché M, Kangasjärvi J, Kaski S.

Bioinformatics. 2012 Sep 15;28(18):2349-56. Epub 2012 Jun 27.

PMID:
22743225
[PubMed - indexed for MEDLINE]
Free Article
13.

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs.

Khan SA, Faisal A, Mpindi JP, Parkkinen JA, Kalliokoski T, Poso A, Kallioniemi OP, Wennerberg K, Kaski S.

BMC Bioinformatics. 2012 May 30;13:112. doi: 10.1186/1471-2105-13-112.

PMID:
22646858
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Identifying fragments of natural speech from the listener's MEG signals.

Koskinen M, Viinikanoja J, Kurimo M, Klami A, Kaski S, Hari R.

Hum Brain Mapp. 2013 Jun;34(6):1477-89. doi: 10.1002/hbm.22004. Epub 2012 Feb 17.

PMID:
22344824
[PubMed - indexed for MEDLINE]
15.

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.

Bioinformatics. 2012 Jan 15;28(2):246-53. doi: 10.1093/bioinformatics/btr634. Epub 2011 Nov 20.

PMID:
22106335
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Metabolic regulation in progression to autoimmune diabetes.

Sysi-Aho M, Ermolov A, Gopalacharyulu PV, Tripathi A, Seppänen-Laakso T, Maukonen J, Mattila I, Ruohonen ST, Vähätalo L, Yetukuri L, Härkönen T, Lindfors E, Nikkilä J, Ilonen J, Simell O, Saarela M, Knip M, Kaski S, Savontaus E, Orešič M.

PLoS Comput Biol. 2011 Oct;7(10):e1002257. doi: 10.1371/journal.pcbi.1002257. Epub 2011 Oct 27.

PMID:
22046124
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy.

Yetukuri L, Huopaniemi I, Koivuniemi A, Maranghi M, Hiukka A, Nygren H, Kaski S, Taskinen MR, Vattulainen I, Jauhiainen M, Orešič M.

PLoS One. 2011;6(8):e23589. doi: 10.1371/journal.pone.0023589. Epub 2011 Aug 24.

PMID:
21887280
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Hierarchical generative biclustering for microRNA expression analysis.

Caldas J, Kaski S.

J Comput Biol. 2011 Mar;18(3):251-61. doi: 10.1089/cmb.2010.0256.

PMID:
21385032
[PubMed - indexed for MEDLINE]
19.

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays.

Lahti L, Elo LL, Aittokallio T, Kaski S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):217-25. doi: 10.1109/TCBB.2009.38.

PMID:
21071809
[PubMed - indexed for MEDLINE]
20.

Global modeling of transcriptional responses in interaction networks.

Lahti L, Knuuttila JE, Kaski S.

Bioinformatics. 2010 Nov 1;26(21):2713-20. doi: 10.1093/bioinformatics/btq500. Epub 2010 Sep 2.

PMID:
20813878
[PubMed - indexed for MEDLINE]
Free Article

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