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Manna, M., Nieminen, T., & Vattulainen, I. (2019). Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes. ANNUAL REVIEW OF BIOPHYSICS, 48, 421-439. https://doi.org/10.1146/annurev-biophys-052118-115553

Liimatainen, K., Kananen, L., Latonen, L., & Ruusuvuori, P. (2019). Iterative unsupervised domain adaptation for generalized cell detection from brightfield z-stacks. BMC Bioinformatics, 20(1), [80]. https://doi.org/10.1186/s12859-019-2605-z

Startceva, S., Kandavalli, V. K., Visa, A., & Ribeiro, A. S. (2019). Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1862(2), 119-128. https://doi.org/10.1016/j.bbagrm.2018.12.005

Laulumaa, S., Nieminen, T., Raasakka, A., Krokengen, O. C., Safaryan, A., Hallin, E. I., ... Kursula, P. (2018). 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, 18(1), [8]. https://doi.org/10.1186/s12900-018-0087-2

Neeli-Venkata, R., Oliveira, S. M. D., Martins, L., Startceva, S., Bahrudeen, M., Fonseca, J. M., ... Ribeiro, A. S. (2018). The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Physical Biology, 15(5), [056002]. https://doi.org/10.1088/1478-3975/aac1cb

Ferreira, A. R. V., Haapanen, J., Mäkelä, J. M., Bratvold, J. E., Nilsen, O., Tuominen, M., ... Coelhoso, I. M. (2017). Comparison of different coating techniques on the properties of FucoPol films. International Journal of Biological Macromolecules, 103, 268-274. https://doi.org/10.1016/j.ijbiomac.2017.05.021

Tripathi, S., Lloyd-Price, J., Ribeiro, A., Yli-Harja, O., Dehmer, M., & Emmert-Streib, F. (2017). sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics, 18(1), [325]. https://doi.org/10.1186/s12859-017-1731-8

Rahmatallah, Y., Zybailov, B., Emmert-Streib, F., & Glazko, G. (2017). GSAR: Bioconductor package for Gene Set analysis in R. BMC Bioinformatics, 18(1), [61]. https://doi.org/10.1186/s12859-017-1482-6

Kandavalli, V. K., Tran, H., & Ribeiro, A. S. (2016). Effects of σ factor competition are promoter initiation kinetics dependent. Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, 1859(10), 1281-1288. https://doi.org/10.1016/j.bbagrm.2016.07.011

Koivuniemi, A., & Vattulainen, I. (2015). Biogenesis of Nascent High Density Lipoprotein Particles. Structure, 23(7), 1153-1154. [3212]. https://doi.org/10.1016/j.str.2015.06.006

Matos Simoes, R. D., Dalleau, S., Williamson, K. E., & Emmert-Streib, F. (2015). Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC Systems Biology, 9, [21]. https://doi.org/10.1186/s12918-015-0165-z

Moriya, T., Acar, E., Cheng, R. H., & Ruotsalainen, U. (2015). A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction. Journal of Structural Biology, 191(3), 318–331. https://doi.org/10.1016/j.jsb.2015.07.007

Rahmatallah, Y., Emmert-Streib, F., & Glazko, G. (2014). Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinformatics, 15(1), [397]. https://doi.org/10.1186/s12859-014-0397-8

Kokkola, T., Suuronen, T., Molnár, F., Määttä, J., Salminen, A., Jarho, E. M., & Lahtela-Kakkonen, M. (2014). AROS has a context-dependent effect on SIRT1. FEBS Letters, 588(9), 1523-1528. https://doi.org/10.1016/j.febslet.2014.03.020

Rangl, M., Leitner, M., Riihimäki, T., Lehtonen, S., Hytönen, V. P., Gruber, H. J., ... Ebner, A. (2014). Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy. Journal of Molecular Recognition, 27(2), 92-97. https://doi.org/10.1002/jmr.2337

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

Anantharajan, J., Koski, M. K., Kursula, P., Hieta, R., Bergmann, U., Myllyharju, J., & Wierenga, R. K. (2013). The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase. Structure, 21(12), 2107-2118. https://doi.org/10.1016/j.str.2013.09.005

Sharma, V., & Misteli, T. (2013). Non-coding RNAs in DNA damage and repair. FEBS Letters, 587(13), 1832-1839. https://doi.org/10.1016/j.febslet.2013.05.006

Tossavainen, H., Helppolainen, S. H., Määttä, J. A. E., Pihlajamaa, T., Hytönen, V. P., Kulomaa, M. S., & Permi, P. (2013). Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms. BIOMOLECULAR NMR ASSIGNMENTS, 7(1), 35-38. https://doi.org/10.1007/s12104-012-9371-4

Lisitsyna, E. S., Durandin, N. A., Ivanov, A. A., Streltsov, S. A., Susova, O. Y., Shtil, A. A., ... Kuzmin, V. A. (2012). Characteristics of complex formation between monomeric and dimeric bisbenzimidazoles and AT-containing polynucleotide. MOLECULAR BIOLOGY, 46(6), 823-827. https://doi.org/10.1134/S0026893312060131

de Matos Simoes, R., Tripathi, S., & Emmert-Streib, F. (2012). Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. BMC Systems Biology, 6, [38]. https://doi.org/10.1186/1752-0509-6-38

Mueller, L. A. J., Kugler, K. G., Graber, A., Emmert-Streib, F., & Dehmer, M. (2011). Structural Measures for Network Biology Using QuACN. BMC Bioinformatics, 12(1), [492]. https://doi.org/10.1186/1471-2105-12-492

Altay, G., & Emmert-Streib, F. (2010). Inferring the conservative causal core of gene regulatory networks. BMC Systems Biology, 4, [132]. https://doi.org/10.1186/1752-0509-4-132

Emmert-Streib, F., & Dehmer, M. (2009). Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC Systems Biology, 3, [76]. https://doi.org/10.1186/1752-0509-3-76

Emmert-Streib, F., & Dehmer, M. (2009). Information processing in the transcriptional regulatory network of yeast: Functional robustness. BMC Systems Biology, 3, [35]. https://doi.org/10.1186/1752-0509-3-35

Dehmer, M., & Emmert-Streib, F. (2008). Structural information content of networks: Graph entropy based on local vertex functionals. Computational Biology and Chemistry, 32(2), 131-138. https://doi.org/10.1016/j.compbiolchem.2007.09.007

Emmert-Streib, F., & Mushegian, A. (2007). A topological algorithm for identification of structural domains of proteins. BMC Bioinformatics, 8, [237]. https://doi.org/10.1186/1471-2105-8-237