Palma, CSD, Kandavalli, V, Bahrudeen, MNM, Minoia, M, Chauhan, V, Dash, S & Ribeiro, AS 2020, 'Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, Vuosikerta. 1863, Nro 5, 194515. https://doi.org/10.1016/j.bbagrm.2020.194515

Vanharanta, L, Peränen, J, Pfisterer, SG, Enkavi, G, Vattulainen, I & Ikonen, E 2020, 'High-content imaging and structure-based predictions reveal functional differences between Niemann-Pick C1 variants', Traffic, Vuosikerta. 21, Nro 5, Sivut 386-397. https://doi.org/10.1111/tra.12727

Liekkinen, J, Enkavi, G, Javanainen, M, Olmeda, B, Pérez-Gil, J & Vattulainen, I 2020, 'Pulmonary Surfactant Lipid Reorganization Induced by the Adsorption of the Oligomeric Surfactant Protein B Complex', JOURNAL OF MOLECULAR BIOLOGY, Vuosikerta. 432, Nro 10, Sivut 3251-3268. https://doi.org/10.1016/j.jmb.2020.02.028

Johansson, JK, Karema-Jokinen, VI, Hakanen, S, Jylhä, A, Uusitalo, H, Vihinen-Ranta, M, Skottman, H, Ihalainen, TO & Nymark, S 2019, 'Sodium channels enable fast electrical signaling and regulate phagocytosis in the retinal pigment epithelium', BMC BIOLOGY, Vuosikerta. 17, Nro 1, 63. https://doi.org/10.1186/s12915-019-0681-1

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, Vuosikerta. 48, Sivut 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, Vuosikerta. 20, Nro 1, 80. https://doi.org/10.1186/s12859-019-2605-z

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

Laulumaa, S, Nieminen, T, Raasakka, A, Krokengen, OC, Safaryan, A, Hallin, EI, Brysbaert, G, Lensink, MF, Ruskamo, S, Vattulainen, 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, Vuosikerta. 18, Nro 1, 8. https://doi.org/10.1186/s12900-018-0087-2

Neeli-Venkata, R, Oliveira, SMD, Martins, L, Startceva, S, Bahrudeen, M, Fonseca, JM, Minoia, M & Ribeiro, AS 2018, 'The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures', Physical Biology, Vuosikerta. 15, Nro 5, 056002. https://doi.org/10.1088/1478-3975/aac1cb

Ferreira, ARV, Haapanen, J, Mäkelä, JM, Bratvold, JE, Nilsen, O, Tuominen, M, Alves, VD & Coelhoso, IM 2017, 'Comparison of different coating techniques on the properties of FucoPol films', International Journal of Biological Macromolecules, Vuosikerta. 103, Sivut 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, Vuosikerta. 18, Nro 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, Vuosikerta. 18, Nro 1, 61. https://doi.org/10.1186/s12859-017-1482-6

Kandavalli, VK, Tran, H & Ribeiro, AS 2016, 'Effects of σ factor competition are promoter initiation kinetics dependent', Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, Vuosikerta. 1859, Nro 10, Sivut 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, Vuosikerta. 23, Nro 7, 3212, Sivut 1153-1154. https://doi.org/10.1016/j.str.2015.06.006

Matos Simoes, RD, Dalleau, S, Williamson, KE & Emmert-Streib, F 2015, 'Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data', BMC Systems Biology, Vuosikerta. 9, 21. https://doi.org/10.1186/s12918-015-0165-z

Moriya, T, Acar, E, Cheng, RH & Ruotsalainen, U 2015, 'A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction', Journal of Structural Biology, Vuosikerta. 191, Nro 3, Sivut 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, Vuosikerta. 15, Nro 1, 397. https://doi.org/10.1186/s12859-014-0397-8

Kokkola, T, Suuronen, T, Molnár, F, Määttä, J, Salminen, A, Jarho, EM & Lahtela-Kakkonen, M 2014, 'AROS has a context-dependent effect on SIRT1', FEBS Letters, Vuosikerta. 588, Nro 9, Sivut 1523-1528. https://doi.org/10.1016/j.febslet.2014.03.020

Rangl, M, Leitner, M, Riihimäki, T, Lehtonen, S, Hytönen, VP, Gruber, HJ, Kulomaa, M, Hinterdorfer, P & Ebner, A 2014, 'Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy', Journal of Molecular Recognition, Vuosikerta. 27, Nro 2, Sivut 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, Dehmer, M & Campbell, F 2014, 'Functional and genetic analysis of the colon cancer network.', BMC Bioinformatics, Vuosikerta. 15, Nro Suppl 6, S6.

Anantharajan, J, Koski, MK, Kursula, P, Hieta, R, Bergmann, U, Myllyharju, J & Wierenga, RK 2013, 'The structural motifs for substrate binding and dimerization of the α subunit of collagen prolyl 4-hydroxylase', Structure, Vuosikerta. 21, Nro 12, Sivut 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, Vuosikerta. 587, Nro 13, Sivut 1832-1839. https://doi.org/10.1016/j.febslet.2013.05.006

Tossavainen, H, Helppolainen, SH, Määttä, JAE, Pihlajamaa, T, Hytönen, VP, Kulomaa, MS & Permi, P 2013, 'Resonance assignments of the 56 kDa chimeric avidin in the biotin-bound and free forms', BIOMOLECULAR NMR ASSIGNMENTS, Vuosikerta. 7, Nro 1, Sivut 35-38. https://doi.org/10.1007/s12104-012-9371-4

Lisitsyna, ES, Durandin, NA, Ivanov, AA, Streltsov, SA, Susova, OY, Shtil, AA, Zhuze, AL & Kuzmin, VA 2012, 'Characteristics of complex formation between monomeric and dimeric bisbenzimidazoles and AT-containing polynucleotide', MOLECULAR BIOLOGY, Vuosikerta. 46, Nro 6, Sivut 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, Vuosikerta. 6, 38. https://doi.org/10.1186/1752-0509-6-38

Mueller, LAJ, Kugler, KG, Graber, A, Emmert-Streib, F & Dehmer, M 2011, 'Structural Measures for Network Biology Using QuACN', BMC Bioinformatics, Vuosikerta. 12, Nro 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, Vuosikerta. 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, Vuosikerta. 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, Vuosikerta. 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, Vuosikerta. 32, Nro 2, Sivut 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, Vuosikerta. 8, 237. https://doi.org/10.1186/1471-2105-8-237