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Ensuring Quality Standards and Reproducible Research for Data Analysis Services in Oncology: A Cooperative Service Model.

Emmert-Streib F, Dehmer M, Yli-Harja O.

Front Cell Dev Biol. 2019 Dec 17;7:349. doi: 10.3389/fcell.2019.00349. eCollection 2019.


Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies.

Intosalmi J, Scott AC, Hays M, Flann N, Yli-Harja O, Lähdesmäki H, Dudley AM, Skupin A.

BMC Mol Cell Biol. 2019 Dec 19;20(1):59. doi: 10.1186/s12860-019-0234-z.


Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation).

Viswanathan A, Musa A, Murugesan A, Vale JR, Afonso CAM, Konda Mani S, Yli-Harja O, Candeias NR, Kandhavelu M.

Cells. 2019 Dec 12;8(12). pii: E1624. doi: 10.3390/cells8121624.


Synthesis and preclinical validation of novel P2Y1 receptor ligands as a potent anti-prostate cancer agent.

Le HTT, Rimpilainen T, Konda Mani S, Murugesan A, Yli-Harja O, Candeias NR, Kandhavelu M.

Sci Rep. 2019 Dec 12;9(1):18938. doi: 10.1038/s41598-019-55194-8.


Utilizing Social Media Data for Psychoanalysis to Study Human Personality.

Emmert-Streib F, Yli-Harja O, Dehmer M.

Front Psychol. 2019 Nov 15;10:2596. doi: 10.3389/fpsyg.2019.02596. eCollection 2019.


Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks.

Musa A, Tripathi S, Dehmer M, Yli-Harja O, Kauffman SA, Emmert-Streib F.

Sci Rep. 2019 May 24;9(1):7849. doi: 10.1038/s41598-019-44291-3.


Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway.

Doan P, Musa A, Candeias NR, Emmert-Streib F, Yli-Harja O, Kandhavelu M.

Front Pharmacol. 2019 Apr 2;10:330. doi: 10.3389/fphar.2019.00330. eCollection 2019.


In vitro anti-glioblastoma activity of L-valine derived boroxazolidones.

Viswanathan A, Sebastianelli G, Brown K, Raunio J, Sipilä V, Yli-Harja O, Candeias NR, Kandhavelu M.

Eur J Pharmacol. 2019 Jul 5;854:194-200. doi: 10.1016/j.ejphar.2019.04.020. Epub 2019 Apr 11.


Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach.

Azam MF, Musa A, Dehmer M, Yli-Harja OP, Emmert-Streib F.

Front Genet. 2019 Feb 14;10:70. doi: 10.3389/fgene.2019.00070. eCollection 2019.


2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma.

Viswanathan A, Kute D, Musa A, Konda Mani S, Sipilä V, Emmert-Streib F, Zubkov FI, Gurbanov AV, Yli-Harja O, Kandhavelu M.

Eur J Med Chem. 2019 Mar 15;166:291-303. doi: 10.1016/j.ejmech.2019.01.021. Epub 2019 Jan 22.


Decane-1,2-diol derivatives as potential antitumor agents for the treatment of glioblastoma.

Viswanathan A, Zhurina A, Assoah B, Paakkunainen A, Musa A, Kute D, Saravanan KM, Yli-Harja O, Candeias NR, Kandhavelu M.

Eur J Pharmacol. 2018 Oct 15;837:105-116. doi: 10.1016/j.ejphar.2018.08.041. Epub 2018 Sep 1.


Anticancer activity study of A3 adenosine receptor agonists.

Marucci G, Santinelli C, Buccioni M, Navia AM, Lambertucci C, Zhurina A, Yli-Harja O, Volpini R, Kandhavelu M.

Life Sci. 2018 Jul 15;205:155-163. doi: 10.1016/j.lfs.2018.05.028. Epub 2018 May 13.


In vitro characterization of arylhydrazones of active methylene derivatives.

Palanivel S, Zhurina A, Doan P, Chandraseelan JG, Khandelwal VKM, Zubkov FI, Mahmudov KT, Pombeiro AJL, Yli-Harja O, Kandhavelu M.

Saudi Pharm J. 2018 Mar;26(3):430-436. doi: 10.1016/j.jsps.2017.12.018. Epub 2018 Jan 2.


In vitro characterization of alkylaminophenols-induced cell death.

Doan P, Anufrieva O, Yli-Harja O, Kandhavelu M.

Eur J Pharmacol. 2018 Feb 5;820:229-234. doi: 10.1016/j.ejphar.2017.12.049. Epub 2017 Dec 21.


Lessons from the Human Genome Project: Modesty, Honesty, and Realism.

Emmert-Streib F, Dehmer M, Yli-Harja O.

Front Genet. 2017 Nov 23;8:184. doi: 10.3389/fgene.2017.00184. eCollection 2017. No abstract available.


Identification of novel GPR17-agonists by structural bioinformatics and signaling activation.

Saravanan KM, Palanivel S, Yli-Harja O, Kandhavelu M.

Int J Biol Macromol. 2018 Jan;106:901-907. doi: 10.1016/j.ijbiomac.2017.08.088. Epub 2017 Aug 18.


Effect of alkylaminophenols on growth inhibition and apoptosis of bone cancer cells.

Doan P, Nguyen T, Yli-Harja O, Candeias NR, Kandhavelu M.

Eur J Pharm Sci. 2017 Sep 30;107:208-216. doi: 10.1016/j.ejps.2017.07.016. Epub 2017 Jul 17.


sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters.

Tripathi S, Lloyd-Price J, Ribeiro A, Yli-Harja O, Dehmer M, Emmert-Streib F.

BMC Bioinformatics. 2017 Jul 4;18(1):325. doi: 10.1186/s12859-017-1731-8.


Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas.

Lehtinen B, Raita A, Kesseli J, Annala M, Nordfors K, Yli-Harja O, Zhang W, Visakorpi T, Nykter M, Haapasalo H, Granberg KJ.

BMC Cancer. 2017 May 3;17(1):310. doi: 10.1186/s12885-017-3274-9.


Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas.

Granberg KJ, Annala M, Lehtinen B, Kesseli J, Haapasalo J, Ruusuvuori P, Yli-Harja O, Visakorpi T, Haapasalo H, Nykter M, Zhang W.

Neuro Oncol. 2017 Sep 1;19(9):1206-1216. doi: 10.1093/neuonc/nox028.


Synthesis of Phenol-derivatives and Biological Screening for Anticancer Activity.

Karjalainen A, Doan P, Chandraseelan JG, Sandberg O, Yli-Harja O, Candeias NR, Kandhavelu M.

Anticancer Agents Med Chem. 2017;17(12):1710-1720. doi: 10.2174/1871520617666170327142027.


A review of connectivity map and computational approaches in pharmacogenomics.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.

Brief Bioinform. 2017 Sep 1;18(5):903. doi: 10.1093/bib/bbx023. No abstract available.


A review of connectivity map and computational approaches in pharmacogenomics.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.

Brief Bioinform. 2018 May 1;19(3):506-523. doi: 10.1093/bib/bbw112. Review. Erratum in: Brief Bioinform. 2017 Sep 1;18(5):903.


Against Dataism and for Data Sharing of Big Biomedical and Clinical Data with Research Parasites.

Emmert-Streib F, Dehmer M, Yli-Harja O.

Front Genet. 2016 Aug 31;7:154. doi: 10.3389/fgene.2016.00154. eCollection 2016. No abstract available.


Synthesis and biological screening for cytotoxic activity of N-substituted indolines and morpholines.

Doan P, Karjalainen A, Chandraseelan JG, Sandberg O, Yli-Harja O, Rosholm T, Franzen R, Candeias NR, Kandhavelu M.

Eur J Med Chem. 2016 Sep 14;120:296-303. doi: 10.1016/j.ejmech.2016.05.024. Epub 2016 May 10.


The Need for Formally Defining "Modern Medicine" by Means of Experimental Design.

Emmert-Streib F, Tuomisto L, Yli-Harja O.

Front Genet. 2016 Apr 20;7:60. doi: 10.3389/fgene.2016.00060. eCollection 2016. No abstract available.


Phase-dependent dynamics of the lac promoter under nutrient stress.

Viswanathan A, Anufrieva O, Sala A, Yli-Harja O, Kandhavelu M.

Res Microbiol. 2016 Jul-Aug;167(6):451-61. doi: 10.1016/j.resmic.2016.04.002. Epub 2016 Apr 19.


Transcriptome Sequencing Reveals PCAT5 as a Novel ERG-Regulated Long Noncoding RNA in Prostate Cancer.

Ylipää A, Kivinummi K, Kohvakka A, Annala M, Latonen L, Scaravilli M, Kartasalo K, Leppänen SP, Karakurt S, Seppälä J, Yli-Harja O, Tammela TL, Zhang W, Visakorpi T, Nykter M.

Cancer Res. 2015 Oct 1;75(19):4026-31. doi: 10.1158/0008-5472.CAN-15-0217. Epub 2015 Aug 17.


Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.

Sala A, Shoaib M, Anufrieva O, Mutharasu G, Jahan Hoque R, Yli-Harja O, Kandhavelu M.

Phys Biol. 2015 May 19;12(3):036003. doi: 10.1088/1478-3975/12/3/036003.


Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling.

Yli-Hietanen J, Ylipää A, Yli-Harja O.

Chin J Cancer. 2015 Apr 11;34(10):423-6. doi: 10.1186/s40880-015-0008-8.


Single-cell kinetics of a repressilator when implemented in a single-copy plasmid.

Oliveira SM, Chandraseelan JG, Häkkinen A, Goncalves NS, Yli-Harja O, Startceva S, Ribeiro AS.

Mol Biosyst. 2015 Jul;11(7):1939-45. doi: 10.1039/c5mb00012b.


Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer.

Annala M, Kivinummi K, Tuominen J, Karakurt S, Granberg K, Latonen L, Ylipää A, Sjöblom L, Ruusuvuori P, Saramäki O, Kaukoniemi KM, Yli-Harja O, Vessella RL, Tammela TL, Zhang W, Visakorpi T, Nykter M.

Oncotarget. 2015 Mar 20;6(8):6235-50.


Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression.

Turner KM, Sun Y, Ji P, Granberg KJ, Bernard B, Hu L, Cogdell DE, Zhou X, Yli-Harja O, Nykter M, Shmulevich I, Yung WK, Fuller GN, Zhang W.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3421-6. doi: 10.1073/pnas.1414573112. Epub 2015 Mar 3.


Origins of transcriptional transition: balance between upstream and downstream regulatory gene sequences.

Sala A, Shoaib M, Anufrieva O, Mutharasu G, Yli-Harja O, Kandhavelu M.

mBio. 2015 Jan 27;6(1). pii: e02182-14. doi: 10.1128/mBio.02182-14.


Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking.

Gupta A, Lloyd-Price J, Oliveira SM, Yli-Harja O, Muthukrishnan AB, Ribeiro AS.

Phys Biol. 2014 Nov 10;11(6):066005. doi: 10.1088/1478-3975/11/6/066005.


Antimicrobial activity and molecular analysis of azoderivatives of β-diketones.

Viswanathan A, Sala A, Yli-Harja O, Kandhavelu M.

Eur J Pharm Sci. 2015 Jan 23;66:83-9. doi: 10.1016/j.ejps.2014.09.020. Epub 2014 Oct 12.


Quantitative analysis of colony morphology in yeast.

Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.

Biotechniques. 2014 Jan;56(1):18-27. doi: 10.2144/000114123.


Effects of multimerization on the temporal variability of protein complex abundance.

Häkkinen A, Tran H, Yli-Harja O, Ingalls B, Ribeiro AS.

BMC Syst Biol. 2013;7 Suppl 1:S3. doi: 10.1186/1752-0509-7-S1-S3. Epub 2013 Aug 12.


Characterization of aberrant pathways across human cancers.

Ylipää A, Yli-Harja O, Zhang W, Nykter M.

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


Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE).

Chowdhury S, Kandhavelu M, Yli-Harja O, Ribeiro AS.

BMC Bioinformatics. 2013;14 Suppl 10:S8. doi: 10.1186/1471-2105-14-S10-S8. Epub 2013 Aug 12.


Multi-scale Gaussian representation and outline-learning based cell image segmentation.

Farhan M, Ruusuvuori P, Emmenlauer M, Rämö P, Dehio C, Yli-Harja O.

BMC Bioinformatics. 2013;14 Suppl 10:S6. doi: 10.1186/1471-2105-14-S10-S6. Epub 2013 Aug 12.


ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.

Annila T, Lihavainen E, Marques IJ, Williams DR, Yli-Harja O, Ribeiro A.

BMC Bioinformatics. 2013;14 Suppl 10:S5. doi: 10.1186/1471-2105-14-S10-S5. Epub 2013 Aug 12.


ESTOOLS Data@Hand: human stem cell gene expression resource.

Kong L, Aho KL, Granberg K, Lund R, Järvenpää L, Seppälä J, Gokhale P, Leinonen K, Hahne L, Mäkelä J, Laurila K, Pukkila H, Närvä E, Yli-Harja O, Andrews PW, Nykter M, Lahesmaa R, Roos C, Autio R.

Nat Methods. 2013 Sep;10(9):814-5. doi: 10.1038/nmeth.2576. No abstract available.


Effects of rate-limiting steps in transcription initiation on genetic filter motifs.

Häkkinen A, Tran H, Yli-Harja O, Ribeiro AS.

PLoS One. 2013 Aug 5;8(8):e70439. doi: 10.1371/journal.pone.0070439. Print 2013.


NanoMiner - integrative human transcriptomics data resource for nanoparticle research.

Kong L, Tuomela S, Hahne L, Ahlfors H, Yli-Harja O, Fadeel B, Lahesmaa R, Autio R.

PLoS One. 2013 Jul 12;8(7):e68414. doi: 10.1371/journal.pone.0068414. Print 2013.


In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter.

Mäkelä J, Kandhavelu M, Oliveira SM, Chandraseelan JG, Lloyd-Price J, Peltonen J, Yli-Harja O, Ribeiro AS.

Nucleic Acids Res. 2013 Jul;41(13):6544-52. doi: 10.1093/nar/gkt350. Epub 2013 May 3.


The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.

Parker BC, Annala MJ, Cogdell DE, Granberg KJ, Sun Y, Ji P, Li X, Gumin J, Zheng H, Hu L, Yli-Harja O, Haapasalo H, Visakorpi T, Liu X, Liu CG, Sawaya R, Fuller GN, Chen K, Lang FF, Nykter M, Zhang W.

J Clin Invest. 2013 Feb;123(2):855-65. doi: 10.1172/JCI67144. Epub 2013 Jan 9.


Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter.

Kandhavelu M, Lloyd-Price J, Gupta A, Muthukrishnan AB, Yli-Harja O, Ribeiro AS.

FEBS Lett. 2012 Nov 2;586(21):3870-5. doi: 10.1016/j.febslet.2012.09.014. Epub 2012 Sep 24.


Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.

Moore LM, Kivinen V, Liu Y, Annala M, Cogdell D, Liu X, Liu CG, Sawaya R, Yli-Harja O, Shmulevich I, Fuller GN, Zhang W, Nykter M.

J Pathol. 2013 Feb;229(3):449-59. doi: 10.1002/path.4109.


Effects of codon sequence on the dynamics of genetic networks.

Potapov I, Mäkelä J, Yli-Harja O, Ribeiro AS.

J Theor Biol. 2012 Dec 21;315:17-25. doi: 10.1016/j.jtbi.2012.08.029. Epub 2012 Aug 31.


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