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Results: 1 to 20 of 97


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(1):12. 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 Apr 29. [Epub ahead of print]


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. 2014 Oct 12;66C:83-89. doi: 10.1016/j.ejps.2014.09.020. [Epub ahead of print]


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.

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