Palma CSD, Kandavalli V, Bahrudeen MNM, Minoia M, Chauhan V, Dash S et al. Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 2020;1863(5). 194515.

Vanharanta L, Peränen J, Pfisterer SG, Enkavi G, Vattulainen I, Ikonen E. High-content imaging and structure-based predictions reveal functional differences between Niemann-Pick C1 variants. Traffic. 2020;21(5):386-397.

Liekkinen J, Enkavi G, Javanainen M, Olmeda B, Pérez-Gil J, Vattulainen I. Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex. JOURNAL OF MOLECULAR BIOLOGY. 2020;432(10):3251-3268.

Johansson JK, Karema-Jokinen VI, Hakanen S, Jylhä A, Uusitalo H, Vihinen-Ranta M et al. Sodium channels enable fast electrical signaling and regulate phagocytosis in the retinal pigment epithelium. BMC BIOLOGY. 2019 elo 15;17(1). 63.

Manna M, Nieminen T, Vattulainen I. Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. ANNUAL REVIEW OF BIOPHYSICS. 2019 touko 6;48:421-439.

Liimatainen K, Kananen L, Latonen L, Ruusuvuori P. Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. BMC Bioinformatics. 2019 helmi 15;20(1). 80.

Startceva S, Kandavalli VK, Visa A, Ribeiro AS. Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 2019 helmi 1;1862(2):119-128.

Laulumaa S, Nieminen T, Raasakka A, Krokengen OC, Safaryan A, Hallin EI et al. Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins. BMC Structural Biology. 2018 kesä 25;18(1). 8.

Neeli-Venkata R, Oliveira SMD, Martins L, Startceva S, Bahrudeen M, Fonseca JM et al. The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Physical Biology. 2018 touko 18;15(5). 056002.

Ferreira ARV, Haapanen J, Mäkelä JM, Bratvold JE, Nilsen O, Tuominen M et al. Comparison of different coating techniques on the properties of FucoPol films. International Journal of Biological Macromolecules. 2017 loka 1;103:268-274.

Tripathi S, Lloyd-Price J, Ribeiro A, Yli-Harja O, Dehmer M, Emmert-Streib F. sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics. 2017 heinä 4;18(1). 325.

Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G. GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics. 2017 tammi 24;18(1). 61.

Kandavalli VK, Tran H, Ribeiro AS. Effects of σ factor competition are promoter initiation kinetics dependent. Biochimica et Biophysica Acta: Gene Regulatory Mechanisms. 2016 loka 1;1859(10):1281-1288.

Koivuniemi A, Vattulainen I. Biogenesis of Nascent High Density Lipoprotein Particles. Structure. 2015 heinä 9;23(7):1153-1154. 3212.

Matos Simoes RD, Dalleau S, Williamson KE, Emmert-Streib F. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC Systems Biology. 2015 touko 14;9. 21.

Moriya T, Acar E, Cheng RH, Ruotsalainen U. A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction. Journal of Structural Biology. 2015 huhti 3;191(3):318–331.

Rahmatallah Y, Emmert-Streib F, Glazko G. Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinformatics. 2014 joulu 5;15(1). 397.

Kokkola T, Suuronen T, Molnár F, Määttä J, Salminen A, Jarho EM et al. AROS has a context-dependent effect on SIRT1. FEBS Letters. 2014 touko 2;588(9):1523-1528.

Rangl M, Leitner M, Riihimäki T, Lehtonen S, Hytönen VP, Gruber HJ et al. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy. Journal of Molecular Recognition. 2014 helmi;27(2):92-97.

Emmert-Streib F, de Matos Simoes R, Glazko G, McDade S, Haibe-Kains B, Holzinger A et al. Functional and genetic analysis of the colon cancer network. BMC Bioinformatics. 2014;15(Suppl 6). S6.

Anantharajan J, Koski MK, Kursula P, Hieta R, Bergmann U, Myllyharju J et al. The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase. Structure. 2013 joulu 3;21(12):2107-2118.

Sharma V, Misteli T. Non-coding RNAs in DNA damage and repair. FEBS Letters. 2013 kesä 27;587(13):1832-1839.

Tossavainen H, Helppolainen SH, Määttä JAE, Pihlajamaa T, Hytönen VP, Kulomaa MS et al. Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms. BIOMOLECULAR NMR ASSIGNMENTS. 2013 huhti;7(1):35-38.

Lisitsyna ES, Durandin NA, Ivanov AA, Streltsov SA, Susova OY, Shtil AA et al. Characteristics of complex formation between monomeric and dimeric bisbenzimidazoles and AT-containing polynucleotide. MOLECULAR BIOLOGY. 2012 marras;46(6):823-827.

de Matos Simoes R, Tripathi S, Emmert-Streib F. Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. BMC Systems Biology. 2012 touko 14;6. 38.

Mueller LAJ, Kugler KG, Graber A, Emmert-Streib F, Dehmer M. Structural Measures for Network Biology Using QuACN. BMC Bioinformatics. 2011 joulu 24;12(1). 492.

Altay G, Emmert-Streib F. Inferring the conservative causal core of gene regulatory networks. BMC Systems Biology. 2010 syys 28;4. 132.

Emmert-Streib F, Dehmer M. Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC Systems Biology. 2009 heinä 20;3. 76.

Emmert-Streib F, Dehmer M. Information processing in the transcriptional regulatory network of yeast: Functional robustness. BMC Systems Biology. 2009 maalis 19;3. 35.

Dehmer M, Emmert-Streib F. Structural information content of networks: Graph entropy based on local vertex functionals. Computational Biology and Chemistry. 2008 huhti;32(2):131-138.

Emmert-Streib F, Mushegian A. A topological algorithm for identification of structural domains of proteins. BMC Bioinformatics. 2007 heinä 3;8. 237.