Eerola SK, Santio NM, Rinne S, Kouvonen P, Corthals GL, Scaravilli M, Scala G, Serra A, Greco D, Ruusuvuori P, Latonen L, Rainio EM, Visakorpi T, Koskinen PJ. 2019. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. CELL COMMUNICATION AND SIGNALING. 17(1). https://doi.org/10.1186/s12964-019-0463-y

Tomkowski R, Sorsa A, Santa-Aho S, Lundin P, Vippola M. 2019. Statistical evaluation of barkhausen noise testing (BNT) for ground samples. Sensors (Switzerland). 19(21). https://doi.org/10.3390/s19214716

Inha LM, Katko TS, Rajala RP. 2019. Improved water services cooperation through clarification of rules and roles. Water (Switzerland). 11(10). https://doi.org/10.3390/w11102172

Saegusa T, Sakai H, Nagashima H, Kobori Y, Tkachenko NV, Hasobe T. 2019. Controlled Orientations of Neighboring Tetracene Units by Mixed Self-Assembled Monolayers on Gold Nanoclusters for High-Yield and Long-Lived Triplet Excited States through Singlet Fission. Journal of the American Chemical Society. 141(37):14720-14727. https://doi.org/10.1021/jacs.9b06567

Li S, Prasanna X, Salo VT, Vattulainen I, Ikonen E. 2019. An efficient auxin-inducible degron system with low basal degradation in human cells. Nature Methods. 16(9):866-869. https://doi.org/10.1038/s41592-019-0512-x

Poojari C, Wilkosz N, Lira RB, Dimova R, Jurkiewicz P, Petka R, Kepczynski M, Róg T. 2019. Behavior of the DPH fluorescence probe in membranes perturbed by drugs. Chemistry and Physics of Lipids. 223. https://doi.org/10.1016/j.chemphyslip.2019.104784

Wang S, Nawale GN, Oommen OP, Hilborn J, Varghese OP. 2019. Influence of ions to modulate hydrazone and oxime reaction kinetics to obtain dynamically cross-linked hyaluronic acid hydrogels. Polymer Chemistry. 10(31):4322-4327. https://doi.org/10.1039/c9py00862d

Pitkänen S, Paakinaho K, Pihlman H, Ahola N, Hannula M, Asikainen S, Manninen M, Morelius M, Keränen P, Hyttinen J, Kellomäki M, Laitinen-Vapaavuori O, Miettinen S. 2019. Characterisation and in vitro and in vivo evaluation of supercritical-CO2-foamed β-TCP/PLCL composites for bone applications. European cells & materials. 38:35-50. https://doi.org/10.22203/eCM.v038a04

Jackson T, Shenkin A, Moore J, Bunce A, van Emmerik T, Kane B, Burcham D, James K, Selker J, Calders K, Origo N, Disney M, Burt A, Wilkes P, Raumonen P, Gonzalez de Tanago Menaca J, Lau A, Herold M, Goodman RC, Fourcaud T, Malhi Y. 2019. An architectural understanding of natural sway frequencies in trees. Journal of the Royal Society. Interface. 16(155). https://doi.org/10.1098/rsif.2019.0116

Ali I, Suominen O, Gotchev A, Morales ER. 2019. Methods for simultaneous robot-world-hand–eye calibration: A comparative study. Sensors (Switzerland). 19(12). https://doi.org/10.3390/s19122837

Habib M, Serebryannikov AE, Caglayan H, Vandenbosch GAE, Ozbay E. 2019. Connection of Collimation, Asymmetric Beaming, and Independent Transmission-Reflection Processes in Concentric-Groove Gratings Supporting Spoof Surface Plasmons. Plasmonics. 14(3):721-729. https://doi.org/10.1007/s11468-018-0850-z

Kekonen A, Bergelin M, Johansson M, Kumar Joon N, Bobacka J, Viik J. 2019. Bioimpedance Sensor Array for Long-Term Monitoring of Wound Healing from Beneath the Primary Dressings and Controlled Formation of H2O2 Using Low-Intensity Direct Current. Sensors. 19(11). https://doi.org/10.3390/s19112505

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

Kerst T, Malmbeck R, lal Banik NL, Toivonen J. 2019. Alpha radiation-induced luminescence by am-241 in aqueous nitric acid solution. Sensors (Switzerland). 19(7). https://doi.org/10.3390/s19071602

Ometov A, Bezzateev S, Davydov V, Shchesniak A, Masek P, Lohan ES, Koucheryavy Y. 2019. Positioning information privacy in intelligent transportation systems: An overview and future perspective. Sensors. 19(7). https://doi.org/10.3390/s19071603

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). 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. 1862(2):119-128. https://doi.org/10.1016/j.bbagrm.2018.12.005

Ylä-Outinen L, Tanskanen JMA, Kapucu FE, Hyysalo A, Hyttinen JAK, Narkilahti S. 2019. Advances in Human Stem Cell-Derived Neuronal Cell Culturing and Analysis. In In Vitro Neuronal Networks: From Culturing Methods to Neuro-Technological Applications. Springer New York LLC. pp. 299-329. (Advances in Neurobiology). https://doi.org/10.1007/978-3-030-11135-9_13

Martins L, Neeli-Venkata R, Oliveira SMD, Häkkinen A, Ribeiro AS, Fonseca JM. 2018. SCIP: a single-cell image processor toolbox. Bioinformatics. 34(24):4318-4320. https://doi.org/10.1093/bioinformatics/bty505

Rinne J, Keskinen J, Berger PR, Lupo D, Valkama M. 2018. M2M Communication Assessment in Energy-Harvesting and Wake-Up Radio Assisted Scenarios Using Practical Components. Sensors (Basel, Switzerland). 18(11). https://doi.org/10.3390/s18113992

Chevrier DM, Raich L, Rovira C, Das A, Luo Z, Yao Q, Chatt A, Xie J, Jin R, Akola J, Zhang P. 2018. Molecular-Scale Ligand Effects in Small Gold-Thiolate Nanoclusters. Journal of the American Chemical Society. 140(45):15430-15436. https://doi.org/10.1021/jacs.8b09440

Mobarak E, Javanainen M, Kulig W, Honigmann A, Sezgin E, Aho N, Eggeling C, Rog T, Vattulainen I. 2018. How to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative. Biochimica et Biophysica Acta - Biomembranes. 1860(11):2436-2445. https://doi.org/10.1016/j.bbamem.2018.07.003

Calderón-Garcidueñas L, González-Maciel A, Reynoso-Robles R, Kulesza RJ, Mukherjee PS, Torres-Jardón R, Rönkkö T, Doty RL. 2018. Alzheimer's disease and alpha-synuclein pathology in the olfactory bulbs of infants, children, teens and adults ≤ 40 years in Metropolitan Mexico City. APOE4 carriers at higher risk of suicide accelerate their olfactory bulb pathology. Environmental Research. 166:348-362. https://doi.org/10.1016/j.envres.2018.06.027

Kartasalo K, Latonen L, Vihinen J, Visakorpi T, Nykter M, Ruusuvuori P. 2018. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics. 34(17):3013-3021. https://doi.org/10.1093/bioinformatics/bty210

Owen MC, Kulig W, Poojari C, Rog T, Strodel B. 2018. Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer. Biochimica et Biophysica Acta - Biomembranes. 1860(9):1709-1720. https://doi.org/10.1016/j.bbamem.2018.03.026

Pirhonen M, Peltokangas M, Vehkaoja A. 2018. Acquiring respiration rate from photoplethysmographic signal by recursive bayesian tracking of intrinsic modes in time-frequency spectra. Sensors. 18(6). https://doi.org/10.3390/s18061693

Virtanen J, Somppi S, Törnqvist H, Jeyhani V, Fiedler P, Gizatdinova Y, Majaranta P, Väätäjä H, Cardó AV, Lekkala J, Tuukkanen S, Surakka V, Vainio O, Vehkaoja A. 2018. Evaluation of dry electrodes in canine heart rate monitoring. Sensors. 18(6). https://doi.org/10.3390/s18061757

George L, Hiltunen A, Santala V, Efimov A. 2018. Photo-antimicrobial efficacy of zinc complexes of porphyrin and phthalocyanine activated by inexpensive consumer LED lamp. Journal of Inorganic Biochemistry. 183:94-100. https://doi.org/10.1016/j.jinorgbio.2018.03.015

Åkerblom M, Raumonen P, Casella E, Disney MI, Danson FM, Gaulton R, Schofield LA, Kaasalainen M. 2018. Non-intersecting leaf insertion algorithm for tree structure models. Interface Focus. 8(2). https://doi.org/10.1098/rsfs.2017.0045

Kaasalainen S, Åkerblom M, Nevalainen O, Hakala T, Kaasalainen M. 2018. Uncertainty in multispectral lidar signals caused by incidence angle effects. Interface Focus. 8(2). https://doi.org/10.1098/rsfs.2017.0033

Disney MI, Boni Vicari M, Burt A, Calders K, Lewis SL, Raumonen P, Wilkes P. 2018. Weighing trees with lasers: Advances, challenges and opportunities. Interface Focus. 8(2). https://doi.org/10.1098/rsfs.2017.0048

Karvinen J, Joki T, Ylä-Outinen L, Koivisto JT, Narkilahti S, Kellomäki M. 2018. Soft hydrazone crosslinked hyaluronan- and alginate-based hydrogels as 3D supportive matrices for human pluripotent stem cell-derived neuronal cells. Reactive and Functional Polymers. 124:29-39. https://doi.org/10.1016/j.reactfunctpolym.2017.12.019

Mehrang S, Pietilä J, Korhonen I. 2018. An activity recognition framework deploying the random forest classifier and a single optical heart rate monitoring and triaxial accelerometer wrist-band. Sensors. 18(2). https://doi.org/10.3390/s18020613

Hakala M, Kalimeri M, Enkavi G, Vattulainen I, Lappalainen P. 2018. Molecular mechanism for inhibition of twinfilin by phosphoinositides. Journal of Biological Chemistry. 293(13):4818-4829. https://doi.org/10.1074/jbc.RA117.000484

Tienaho J, Poikulainen E, Sarjala T, Muilu-Mäkelä R, Santala V, Karp M. 2018. A Bioscreening Technique for Ultraviolet Irradiation Protective Natural Substances. Photochemistry and Photobiology. 94(6):1273-1280. https://doi.org/10.1111/php.12954

Ojansivu M, Wang X, Hyväri L, Kellomäki M, Hupa L, Vanhatupa S, Miettinen S. 2018. Bioactive glass induced osteogenic differentiation of human adipose stem cells is dependent on cell attachment mechanism and mitogen-activated protein kinases. European Cells and Materials. 35:53-71. https://doi.org/10.22203/eCM.v035a05

Khanongnuch R, Di Capua F, Lakaniemi A-M, Rene ER, Lens PNL. 2018. Effect of N/S ratio on anoxic thiosulfate oxidation in a fluidized bed reactor: Experimental and artificial neural network model analysis. Process Biochemistry. 68:171-181. https://doi.org/10.1016/j.procbio.2018.02.018

Rokade SS, Joshi KA, Mahajan K, Patil S, Tomar G, Dubal DS, Parihar VS, Kitture R, Bellare JR, Ghosh S. 2018. Gloriosa superba Mediated Synthesis of Platinum and Palladium Nanoparticles for Induction of Apoptosis in Breast Cancer. Bioinorganic Chemistry and Applications. 2018. https://doi.org/10.1155/2018/4924186

Fedele C, De Gregorio M, Netti PA, Cavalli S, Attanasio C. 2017. Azopolymer photopatterning for directional control of angiogenesis. Acta Biomaterialia. 63:317-325. https://doi.org/10.1016/j.actbio.2017.09.022

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. 103:268-274. https://doi.org/10.1016/j.ijbiomac.2017.05.021

Sciacca MFM, Romanucci V, Zarrelli A, Monaco I, Lolicato F, Spinella N, Galati C, Grasso G, D'Urso L, Romeo M, Diomede L, Salmona M, Bongiorno C, Di Fabio G, La Rosa C, Milardi D. 2017. Inhibition of Aβ Amyloid Growth and Toxicity by Silybins: The Crucial Role of Stereochemistry. ACS Chemical Neuroscience. 8(8):1767-1778. https://doi.org/10.1021/acschemneuro.7b00110

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). https://doi.org/10.1186/s12859-017-1731-8

Nogueira IBR, Ribeiro AM, Martins MAF, Rodrigues AE, Koivisto H, Loureiro JM. 2017. Dynamics of a True Moving Bed separation process: Linear model identification and advanced process control. Journal of Chromatography A. 1504. https://doi.org/10.1016/j.chroma.2017.04.060

Mokkila S, Postila PA, Rissanen S, Juhola H, Vattulainen I, Róg T. 2017. Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles. ACS Chemical Neuroscience. 8(6):1242-1250. https://doi.org/10.1021/acschemneuro.6b00395

Manna M, Javanainen M, Martinez-Seara Monne H, Gabius H-J, Rog T, Vattulainen I. 2017. Long-chain GM1 gangliosides alter transmembrane domain registration through interdigitation. Biochimica et Biophysica Acta: Biomembranes. 1859(5):870-878. https://doi.org/10.1016/j.bbamem.2017.01.033

Kahraman M, Ozbay A, Yuksel H, Solmaz R, Demir B, Caglayan H. 2017. Tunable Plasmonic Silver Nanodomes for Surface-Enhanced Raman Scattering. Plasmonics. 1-11. https://doi.org/10.1007/s11468-017-0573-6

Higashino T, Nakatsuji H, Fukuda R, Okamoto H, Imai H, Matsuda T, Tochio H, Shirakawa M, Tkachenko NV, Hashida M, Murakami T, Imahori H. 2017. Hexaphyrin as a Potential Theranostic Dye for Photothermal Therapy and 19F Magnetic Resonance Imaging. ChemBioChem. 18(10):951-959. https://doi.org/10.1002/cbic.201700071

Bilkova E, Pleskot R, Rissanen S, Sun S, Czogalla A, Cwiklik L, Róg T, Vattulainen I, Cremer PS, Jungwirth P, Coskun Ü. 2017. Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. Journal of the American Chemical Society. 139(11):4019-4024. https://doi.org/10.1021/jacs.6b11760

Milani R, Houbenov N, Fernandez-Palacio F, Cavallo G, Luzio A, Haataja J, Giancane G, Saccone M, Priimägi A, Metrangolo P, Ikkala O. 2017. Hierarchical Self-Assembly of Halogen-Bonded Block Copolymer Complexes into Upright Cylindrical Domains. CheM. 2(3):417-426. https://doi.org/10.1016/j.chempr.2017.02.003

Euro L, Haapanen O, Róg T, Vattulainen I, Suomalainen A, Sharma V. 2017. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis. Biochemistry. 56(9):1227-1238. https://doi.org/10.1021/acs.biochem.6b00934

Balanta MAG, Orsi Gordo V, Carvalho ARH, Puustinen J, Alghamdi HM, Henini M, Galeti HVA, Guina M, Galvão Gobato Y. 2017. Polarization resolved photoluminescence in GaAs1−xBix/GaAs quantum wells. Journal of Luminescence. 182:49-52. https://doi.org/10.1016/j.jlumin.2016.10.008

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

Grabon A, Orłowski A, Tripathi A, Vuorio J, Javanainen M, Róg T, Lönnfors M, McDermott MI, Siebert G, Somerharju P, Vattulainen I, Bankaitis VA. 2017. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle. Journal of Biological Chemistry. 292(35):14438-14455. https://doi.org/10.1074/jbc.M117.791467

Lahbib I, Valkonen A, Rzaigui M, Smirani W. 2017. Synthesis, Structural Characterization, Hirshfeld Surface and Antioxidant Activity Analysis of a Novel Organic Cation Antimonate Complex. Journal of Cluster Science. 28(4):2239–2252. https://doi.org/10.1007/s10876-017-1217-x

Stupnikov A, Tripathi S, De Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. 2016. SamExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 32(21):3345-3347. https://doi.org/10.1093/bioinformatics/btw475

Kandavalli VK, Tran H, Ribeiro AS. 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

Kuleta P, Sarewicz M, Postila P, Róg T, Osyczka A. 2016. Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1. Biochimica et Biophysica Acta: Bioenergetics. 1857(10):1661-1668. https://doi.org/10.1016/j.bbabio.2016.07.003

Vattulainen I, Róg T. 2016. Lipid membranes: Theory and simulations bridged to experiments. Biochimica et Biophysica Acta: Biomembranes. 1858(10):2251-2253. https://doi.org/10.1016/j.bbamem.2016.06.007

Javanainen M, Martinez-Seara H. 2016. Efficient preparation and analysis of membrane and membrane protein systems. Biochimica et Biophysica Acta: Biomembranes. 1858(10):2468-2482. https://doi.org/10.1016/j.bbamem.2016.02.036

Kepczynski M, Róg T. 2016. Functionalized lipids and surfactants for specific applications. Biochimica et Biophysica Acta: Biomembranes. 1858(10):2362-2379. https://doi.org/10.1016/j.bbamem.2016.02.038

Kaurola P, Sharma V, Vonk A, Vattulainen I, Róg T. 2016. Distribution and dynamics of quinones in the lipid bilayer mimicking the inner membrane of mitochondria. Biochimica et Biophysica Acta: Biomembranes. 1858(9):2116-2122. https://doi.org/10.1016/j.bbamem.2016.06.016

Sharma V, Wikström M. 2016. The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta: Bioenergetics. 1857(8):1111-1115. https://doi.org/10.1016/j.bbabio.2016.02.008

Razavi A, Valkama M, Lohan ES. 2016. Robust statistical approaches for RSS-based floor detection in indoor localization. Sensors. 16(6). https://doi.org/10.3390/s16060793

Häkkinen A, Ribeiro AS. 2016. Characterizing rate limiting steps in transcription from RNA production times in live cells. Bioinformatics. 32(9):1346-1352. https://doi.org/10.1093/bioinformatics/btv744

Vuornos K, Björninen M, Talvitie E, Paakinaho K, Kellomäki M, Huhtala H, Miettinen S, Seppänen-Kaijansinkko R, Haimi S. 2016. Human Adipose Stem Cells Differentiated on Braided Polylactide Scaffolds is a Potential Approach for Tendon Tissue Engineering. Tissue Engineering Part A. 22(5-6):513-523. https://doi.org/10.1089/ten.tea.2015.0276

Kulig W, Cwiklik L, Jurkiewicz P, Rog T, Vattulainen I. 2016. Cholesterol oxidation products and their biological importance. Chemistry and Physics of Lipids. 199:144-160. https://doi.org/10.1016/j.chemphyslip.2016.03.001

Teppola H, Sarkanen JR, Jalonen TO, Linne M-L. 2016. Morphological Differentiation Towards Neuronal Phenotype of SH-SY5Y Neuroblastoma Cells by Estradiol, Retinoic Acid and Cholesterol. Neurochemical Research. 41(4):731-747. https://doi.org/10.1007/s11064-015-1743-6

Metzler R, Jeon JH, Cherstvy AG. 2016. Non-Brownian diffusion in lipid membranes: Experiments and simulations. Biochimica et Biophysica Acta: Biomembranes. 215:173–185. https://doi.org/10.1016/j.bbamem.2016.01.022

Pöyry S, Vattulainen I. 2016. Role of charged lipids in membrane structures: Insight given by simulations. Biochimica et Biophysica Acta: Biomembranes. 2322–2333. https://doi.org/10.1016/j.bbamem.2016.03.016

Rog T, Koivuniemi A. 2016. The biophysical properties of ethanolamine plasmalogens revealed by atomistic molecular dynamics simulations. Biochimica et Biophysica Acta: Biomembranes. 1858(1):97-103. https://doi.org/10.1016/j.bbamem.2015.10.023

Jia L, Sun Z, Wu X, Misteli T, Sharma V. 2015. Gene expression analysis upon lncRNA DDSR1 knockdown in human fibroblasts. Genomics Data. 6:277-279. https://doi.org/10.1016/j.gdata.2015.10.017

Ravi A, Luthra A, Teixeira FL, Berger PR, Coe JV. 2015. Tuning the Plasmonic Extinction Resonances of Hexagonal Arrays of Ag Nanoparticles. Plasmonics. 10(6):1505-1512. https://doi.org/10.1007/s11468-015-9963-9

Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. 2015. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO REPORTS. 16(11):1520-1534. https://doi.org/10.15252/embr.201540437

Vapaavuori J, Laventure A, Bazuin CG, Lebel O, Pellerin C. 2015. Submolecular Plasticization Induced by Photons in Azobenzene Materials. Journal of the American Chemical Society. 137(42):13510-13517. https://doi.org/10.1021/jacs.5b06611

Ryödi E, Metso S, Jaatinen P, Huhtala H, Saaristo R, Välimäki M, Auvinen A. 2015. Cancer incidence and mortality in patients treated either with RAI or thyroidectomy for hyperthyroidism. Journal of Clinical Endocrinology and Metabolism. 100(10):3710-3717. https://doi.org/10.1210/jc.2015-1874

Sorkio A, Porter PJ, Juuti-Uusitalo K, Meenan BJ, Skottman H, Burke GA. 2015. Surface Modified Biodegradable Electrospun Membranes as a Carrier for Human Embryonic Stem Cell-Derived Retinal Pigment Epithelial Cells. Tissue Engineering Part A. 21(17-18):2301-2314. https://doi.org/10.1089/ten.tea.2014.0640

Ojansivu M, Vanhatupa S, Björkvik L, Häkkänen H, Kellomäki M, Autio R, Ihalainen JA, Hupa L, Miettinen S. 2015. Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells. Acta Biomaterialia. 21:190-203. https://doi.org/10.1016/j.actbio.2015.04.017

Rodrigues PC, Monteiro A, Lourenço VM. 2015. A robust AMMI model for the analysis of genotype-by-environment data. Bioinformatics. 32(1):58-66. https://doi.org/10.1093/bioinformatics/btv533

Kulig W, Olzyńska A, Jurkiewicz P, Kantola AM, Komulainen S, Manna M, Pourmousa M, Vazdar M, Cwiklik L, Rog T, Khelashvili G, Harries D, Telkki VV, Hof M, Vattulainen I, Jungwirth P. 2015. Cholesterol under oxidative stress: How lipid membranes sense oxidation as cholesterol is being replaced by oxysterols. Free Radical Biology and Medicine. 84:30-41. https://doi.org/10.1016/j.freeradbiomed.2015.03.006

Nguyen SD, Javanainen M, Rissanen S, Zhao H, Huusko J, Kivelä AM, Ylä-Herttuala S, Navab M, Fogelman AM, Vattulainen I, Kovanen PT, Öörni K. 2015. Apolipoprotein A-I mimetic peptide 4F blocks sphingomyelinase-induced LDL aggregation. Journal of Lipid Research. 56(6):1206-1221. https://doi.org/10.1194/jlr.M059485

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. 2015. Using shRNA experiments to validate gene regulatory networks. Genomics Data. 4:123-126. https://doi.org/10.1016/j.gdata.2015.03.011

Sharma V, Ala-Vannesluoma P, Vattulainen I, Wikström M, Róg T. 2015. Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta: Bioenergetics. 1847(8):690-697. https://doi.org/10.1016/j.bbabio.2015.04.007

Potapov I, Zhurov B, Volkov E. 2015. Multi-stable dynamics of the non-adiabatic repressilator. Journal of the Royal Society. Interface. 12(104). https://doi.org/10.1098/rsif.2014.1315

Schroeder CA, Pluharová E, Seidel R, Schroeder WP, Faubel M, Slavíçek P, Winter B, Jungwirth P, Bradforth SE. 2015. Oxidation half-reaction of aqueous nucleosides and nucleotides via photoelectron spectroscopy augmented by ab initio calculations. Journal of the American Chemical Society. 137(1):201-209. https://doi.org/10.1021/ja508149e

Häkkinen A, Ribeiro AS. 2015. Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinformatics. 31(1):69-75. https://doi.org/10.1093/bioinformatics/btu592

Lehtonen SI, Taskinen B, Ojala E, Kukkurainen S, Rahikainen R, Riihimäki TA, Laitinen OH, Kulomaa MS, Hytönen VP. 2015. Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning. Protein Engineering Design and Selection. 28(1):23-28. https://doi.org/10.1093/protein/gzu050

Kulig W, Jurkiewicz P, Olzyńska A, Tynkkynen J, Javanainen M, Manna M, Rog T, Hof M, Vattulainen I, Jungwirth P. 2015. Experimental determination and computational interpretation of biophysical properties of lipid bilayers enriched by cholesteryl hemisuccinate. Biochimica et Biophysica Acta: Biomembranes. 1848(2):422-432. https://doi.org/10.1016/j.bbamem.2014.10.032

Akimova AV, Rychkov GN, Grin MA, Filippova NA, Golovina GV, Durandin NA, Vinogradov AM, Kokrashvili TA, Mironov AF, Shtil AA, Kuzmin VA. 2015. Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives. ACTA NATURAE. 7(1):109-116.

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

Takala H, Lehtivuori H, Hammarén H, Hytönen VP, Ihalainen JA. 2014. Connection between absorption properties and conformational changes in Deinococcus radiodurans phytochrome. Biochemistry. 53(45):7076-7085. https://doi.org/10.1021/bi501180s

Deng Y, Alicea-Velázquez NL, Bannwarth L, Lehtonen SI, Boggon TJ, Cheng HC, Hytönen VP, Turk BE. 2014. Global analysis of human nonreceptor tyrosine kinase specificity using high-density peptide microarrays. Journal of Proteome Research. 13(10):4339-4346. https://doi.org/10.1021/pr500503q

Spencer CI, Baba S, Nakamura K, Hua EA, Sears MAF, Fu CC, Zhang J, Balijepalli S, Tomoda K, Hayashi Y, Lizarraga P, Wojciak J, Scheinman MM, Aalto-Setälä K, Makielski JC, January CT, Healy KE, Kamp TJ, Yamanaka S, Conklin BR. 2014. Calcium transients closely reflect prolonged action potentials in iPSC models of inherited cardiac arrhythmia. Stem Cell Reports. 3(2):269-281. https://doi.org/10.1016/j.stemcr.2014.06.003

Raitoharju E, Seppälä I, Oksala N, Lyytikäinen LP, Raitakari O, Viikari J, Ala-Korpela M, Soininen P, Kangas AJ, Waldenberger M, Klopp N, Illig T, Leiviskä J, Loo BM, Hutri-Kähönen N, Kähönen M, Laaksonen R, Lehtimäki T. 2014. Blood microRNA profile associates with the levels of serum lipids and metabolites associated with glucose metabolism and insulin resistance and pinpoints pathways underlying metabolic syndrome. The cardiovascular risk in Young Finns Study. Molecular and Cellular Endocrinology. 391(1-2):41-49. https://doi.org/10.1016/j.mce.2014.04.013

Koskela JE, Liljeström V, Lim J, Simanek EE, Ras RHA, Priimagi A, Kostiainen MA. 2014. Light-fuelled transport of large dendrimers and proteins. Journal of the American Chemical Society. 136(19):6850-6853. https://doi.org/10.1021/ja502623m

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. 588(9):1523-1528. https://doi.org/10.1016/j.febslet.2014.03.020

Tripathi S, Dehmer M, Emmert-Streib F. 2014. NetBioV: An R package for visualizing large network data in biology and medicine. Bioinformatics. 30(19):2834-2836. https://doi.org/10.1093/bioinformatics/btu384

Mikhailova A, Ilmarinen T, Uusitalo H, Skottman H. 2014. Small-molecule induction promotes corneal epithelial cell differentiation from human induced pluripotent stem cells. Stem Cell Reports. 2(2):219-231. https://doi.org/10.1016/j.stemcr.2013.12.014

Rahmatallah Y, Emmert-Streib F, Glazko G. 2014. Gene Sets Net Correlations Analysis (GSNCA): A multivariate differential coexpression test for gene sets. Bioinformatics. 30(3):360-368. https://doi.org/10.1093/bioinformatics/btt687

Sorkio A, Hongisto H, Kaarniranta K, Uusitalo H, Juuti-Uusitalo K, Skottman H. 2014. Structure and barrier properties of human embryonic stem cell-derived retinal pigment epithelial cells are affected by extracellular matrix protein coating. Tissue Engineering Part A. 20(3-4):622-634. https://doi.org/10.1089/ten.tea.2013.0049

Ji J, Sharma V, Qi S, Guarch ME, Zhao P, Luo Z, Fan W, Wang Y, Mbabaali F, Neculai D, Esteban MA, McPherson JD, Batada NN. 2014. Antioxidant supplementation reduces genomic aberrations in human induced pluripotent stem cells. Stem Cell Reports. 2(1):44-51. https://doi.org/10.1016/j.stemcr.2013.11.004

Oksala NKJ, Ekmekçi FG, Özsoy E, Kirankaya Ş, Kokkola T, Emecen G, Lappalainen J, Kaarniranta K, Atalay M. 2014. Natural thermal adaptation increases heat shock protein levels and decreases oxidative stress. REDOX BIOLOGY. 3:25-28. https://doi.org/10.1016/j.redox.2014.10.003

Maria Cherian R, Gaunitz S, Nilsson A, Liu J, Karlsson NG, Holgersson J. 2014. Shiga-like toxin binds with high avidity to multivalent O-linked blood group P1 determinants on mucin-type fusion proteins. GLYCOBIOLOGY. 24(1):26-38. https://doi.org/10.1093/glycob/cwt086

Křížek T, Kubíčková A, Hladílková J, Coufal P, Heyda J, Jungwirth P. 2014. Electrophoretic mobilities of neutral analytes and electroosmotic flow markers in aqueous solutions of Hofmeister salts. ELECTROPHORESIS. 35(5):617-624. https://doi.org/10.1002/elps.201300544

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. 15(Suppl 6).

Näreoja T, Ebner A, Gruber HJ, Taskinen B, Kienberger F, Hänninen PE, Hytönen VP, Hinterdorfer P, Härmä H. 2014. Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay. Analytical and Bioanalytical Chemistry. 406(2):493-503. https://doi.org/10.1007/s00216-013-7474-0

Akimova AV, Grin MA, Golovina GV, Kokrashvili TA, Vinogradov AM, Mironov AF, Rychkov GN, Shtil AA, Kuzmin VA, Durandin NA. 2014. Novel derivatives of bacteriochlorophyll a: Complex formation with albumin and the mechanism of tumor cell photodamage. DOKLADY BIOCHEMISTRY AND BIOPHYSICS. 454(1):17-20. https://doi.org/10.1134/S1607672914010062

Hakala T, Sand J, Kellokumpu-Lehtinen PL, Huhtala H, Leinonen R, Kholová I. 2014. Recurrent thyroid cancers have more peritumoural lymphatic vasculature than nonrecurrent thyroid cancers. European Journal of Clinical Investigation. 44(9):825-832. https://doi.org/10.1111/eci.12301

Emmert-Streib F, Zhang SD, Hamilton P. 2014. Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast. Genomics Data. 2:37-39. https://doi.org/10.1016/j.gdata.2013.12.001

Häkkinen MR, Roine A, Auriola S, Tuokko A, Veskimäe E, Keinänen TA, Lehtimäki T, Oksala N, Vepsäläinen J. 2013. Analysis of free, mono- and diacetylated polyamines from human urine by LC-MS/MS. JOURNAL OF CHROMATOGRAPHY B: ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES. 941:81-89. https://doi.org/10.1016/j.jchromb.2013.10.009

Stirnemann G, Wernersson E, Jungwirth P, Laage D. 2013. Mechanisms of acceleration and retardation of water dynamics by ions. Journal of the American Chemical Society. 135(32):11824-11831. https://doi.org/10.1021/ja405201s

Chen J, Xi J, Tian Y, Bova GS, Zhang H. 2013. Identification, prioritization, and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens. Proteomics. 13(15):2268-2277. https://doi.org/10.1002/pmic.201200541

Diban N, Haimi S, Bolhuis-Versteeg L, Teixeira S, Miettinen S, Poot A, Grijpma D, Stamatialis D. 2013. Development and characterization of poly(ε-caprolactone) hollow fiber membranes for vascular tissue engineering. Journal of Membrane Science. 438:29-37. https://doi.org/10.1016/j.memsci.2013.03.024

Leppiniemi J, Meir A, Kahkonen N, Kukkurainen S, Maatta JA, Ojanen M, Janis J, Kulomaa MS, Livnah O, Hytonen VP. 2013. The highly dynamic oligomeric structure of bradavidin II is unique among avidin proteins. PROTEIN SCIENCE. 22(7):980-994. https://doi.org/10.1002/pro.2281

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 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. 7(1):35-38. https://doi.org/10.1007/s12104-012-9371-4

Poojari C, Kukol A, Strodel B. 2013. How the amyloid-β peptide and membranes affect each other: An extensive simulation study. Biochimica et Biophysica Acta: Biomembranes. 1828(2):327-339. https://doi.org/10.1016/j.bbamem.2012.09.001

Shaikh SA, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. 2013. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry. 52(4):569-587. https://doi.org/10.1021/bi301086x

Diban N, Haimi S, Bolhuis-Versteeg L, Teixeira S, Miettinen S, Poot A, Grijpma D, Stamatialis D. 2013. Hollow fibers of poly(lactide-co-glycolide) and poly(ε-caprolactone) blends for vascular tissue engineering applications. Acta Biomaterialia. 9(5):6450-6458. https://doi.org/10.1016/j.actbio.2013.01.005

Ylilauri M, Mattila E, Nurminen EM, Käpylä J, Niinivehmas SP, Määttä JA, Pentikäinen U, Ivaska J, Pentikäinen OT. 2013. Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone. Biochimica et biophysica acta: proteins and proteomics. 1834(10):1988-1997. https://doi.org/10.1016/j.bbapap.2013.07.001

Rahmatallah Y, Emmert-Streib F, Glazko G. 2012. Gene set analysis for self-contained tests: Complex null and specific alternative hypotheses. Bioinformatics. 28(23):3073-3080. https://doi.org/10.1093/bioinformatics/bts579

Jurkiewicz P, Olzyńska A, Cwiklik L, Conte E, Jungwirth P, Megli FM, Hof M. 2012. Biophysics of lipid bilayers containing oxidatively modified phospholipids: Insights from fluorescence and EPR experiments and from MD simulations. Biochimica et Biophysica Acta: Biomembranes. 1818(10):2388-2402. https://doi.org/10.1016/j.bbamem.2012.05.020

Tammela TLJ. 2012. Endocrine prevention and treatment of prostate cancer. Molecular and Cellular Endocrinology. 360(1-2):59-67. https://doi.org/10.1016/j.mce.2012.03.002

Rembert KB, Paterová J, Heyda J, Hilty C, Jungwirth P, Cremer PS. 2012. Molecular mechanisms of ion-specific effects on proteins. Journal of the American Chemical Society. 134(24):10039-10046. https://doi.org/10.1021/ja301297g

Sharma V, Bala A, Deshmukh R, Bedi KL, Sharma PL. 2012. Neuroprotective effect of RO-20-1724-a phosphodiesterase4 inhibitor against intracerebroventricular streptozotocin induced cognitive deficit and oxidative stress in rats. PHARMACOLOGY BIOCHEMISTRY AND BEHAVIOR. 101(2):239-245. https://doi.org/10.1016/j.pbb.2012.01.004

Jääskeläinen T, Makkonen H, Visakorpi T, Kim J, Roeder RG, Palvimo JJ. 2012. Histone H2B ubiquitin ligases RNF20 and RNF40 in androgen signaling and prostate cancer cell growth. Molecular and Cellular Endocrinology. 350(1):87-98. https://doi.org/10.1016/j.mce.2011.11.025

Wernersson E, Heyda J, Kubíčková A, Křížek T, Coufal P, Jungwirth P. 2012. Counterion condensation in short cationic peptides: Limiting mobilities beyond the Onsager-Fuoss theory. ELECTROPHORESIS. 33(6):981-989. https://doi.org/10.1002/elps.201100602

Usvalampi A, Turunen O, Valjakka J, Pastinen O, Leisola M, Nyyssölä A. 2012. Production of l-xylose from l-xylulose using Escherichia coli l-fucose isomerase. ENZYME AND MICROBIAL TECHNOLOGY. 50(1):71-76. https://doi.org/10.1016/j.enzmictec.2011.09.009

Sarkanen JR, Kaila V, Mannerström B, Räty S, Kuokkanen H, Miettinen S, Ylikomi T. 2012. Human adipose tissue extract induces angiogenesis and adipogenesis in vitro. Tissue Engineering Part A. 18(1-2):17-25. https://doi.org/10.1089/ten.tea.2010.0712

Jurkiewicz P, Cwiklik L, Jungwirth P, Hof M. 2012. Lipid hydration and mobility: An interplay between fluorescence solvent relaxation experiments and molecular dynamics simulations. Biochimie. 94(1):26-32. https://doi.org/10.1016/j.biochi.2011.06.027

Tirkkonen L, Haimi S, Huttunen S, Wolff J, Pirhonen E, Sándor GK, Miettinen S. 2012. Osteogenic medium is superior to growth factors in differentiation of human adipose stem cells towards boneforming cells in 3D culture. European Cells and Materials. 25:144-158.

Grönholm J, Vanhatupa S, Ungureanu D, Väliaho J, Laitinen T, Valjakka J, Silvennoinen O. 2012. Structure-function analysis indicates that sumoylation modulates DNA-binding activity of STAT1. BMC BIOCHEMISTRY. 13(1). https://doi.org/10.1186/1471-2091-13-20

Mueller LAJ, Kugler KG, Graber A, Emmert-Streib F, Dehmer M. 2011. Structural Measures for Network Biology Using QuACN. BMC Bioinformatics. 12(1). https://doi.org/10.1186/1471-2105-12-492

Tevyashova AN, Shtil AA, Olsufyeva EN, Luzikov YN, Reznikova MI, Dezhenkova LG, Isakova EB, Bukhman VM, Durandin NA, Vinogradov AM, Kuzmin VA, Preobrazhenskaya MN. 2011. Modification of olivomycin A at the side chain of the aglycon yields the derivative with perspective antitumor characteristics. BIOORGANIC AND MEDICINAL CHEMISTRY. 19(24):7387-7393. https://doi.org/10.1016/j.bmc.2011.10.055

Heger M, Salles II, Bezemer R, Cloos MA, Mordon SR, Bégu S, Deckmyn H, Beek JF. 2011. Laser-induced primary and secondary hemostasis dynamics and mechanisms in relation to selective photothermolysis of port wine stains. JOURNAL OF DERMATOLOGICAL SCIENCE. 63(3):139-147. https://doi.org/10.1016/j.jdermsci.2011.04.015

Sharma V, Wikström M, Kaila VRI. 2011. Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb3. Biochimica et Biophysica Acta: Bioenergetics. 1807(7):813-818. https://doi.org/10.1016/j.bbabio.2011.02.002

Yu G, Zhang B, Bova GS, Xu J, Shih IM, Wang Y. 2011. BACOM: In silico detection of genomic deletion types and correction of normal cell contamination in copy number data. Bioinformatics. 27(11):1473-1480. https://doi.org/10.1093/bioinformatics/btr183

Heikkilä E, Ristola M, Havana M, Jones N, Holthöfer H, Lehtonen S. 2011. Trans-interaction of nephrin and Neph1/Neph3 induces cell adhesion that associates with decreased tyrosine phosphorylation of nephrin. BIOCHEMICAL JOURNAL. 435(3):619-628. https://doi.org/10.1042/BJ20101599

Auer S, Nirschl M, Schreiter M, Vikholm-Lundin I. 2011. Detection of DNA hybridisation in a diluted serum matrix by surface plasmon resonance and film bulk acoustic resonators. Analytical and Bioanalytical Chemistry. 400(5):1387-1396. https://doi.org/10.1007/s00216-011-4871-0

Kaila VRI, Sharma V, Wikström M. 2011. The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase. Biochimica et Biophysica Acta: Bioenergetics. 1807(1):80-84. https://doi.org/10.1016/j.bbabio.2010.08.014

Dantelle G, Slablab A, Rondin L, Lainé F, Carrel F, Bergonzo P, Perruchas S, Gacoin T, Treussart F, Roch JF. 2010. Efficient production of NV colour centres in nanodiamonds using high-energy electron irradiation. Journal of Luminescence. 130(9):1655-1658. https://doi.org/10.1016/j.jlumin.2009.12.003

Altay G, Emmert-Streib F. 2010. Revealing differences in gene network inference algorithms on the network level by ensemble methods. Bioinformatics. 26(14):1738-1744. https://doi.org/10.1093/bioinformatics/btq259

Kanninen L, Jokinen N, Lahtonen K, Jussila P, Ali-Löytty H, Hirsimäki M, Leppiniemi J, Hytönen V, Kulomaa M, Ahola N, Paakinaho K, Kellomäki M, Valden M. 2010. Surface science analysis and surface modification methods for biomaterials research. European Cells and Materials. 20(SUPPL. 3):133.

Glazko GV, Emmert-Streib F. 2009. Unite and conquer: Univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics. 25(18):2348-2354. https://doi.org/10.1093/bioinformatics/btp406

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

Einola JKM, Kettunen RH, Rintala JA. 2007. Responses of methane oxidation to temperature and water content in cover soil of a boreal landfill. Soil Biology and Biochemistry. 39(5):1156-1164. https://doi.org/10.1016/j.soilbio.2006.12.022

Lokshina LY, Vavilin VA, Salminen E, Rintala J. 2003. Modeling of anaerobic degradation of solid slaughterhouse waste: Inhibition effects of long-chain fatty acids or ammonia. Applied Biochemistry and Biotechnology. 109(1-3):15-32. https://doi.org/10.1385/ABAB:109:1-3:15

Tois J, Franzén R, Aitio O, Huikko K, Taskinen J. 2000. Preparation of 5-substituted 2-carboxyindoles on solid support. Tetrahedron Letters. 41(14):2443-2446. https://doi.org/10.1016/S0040-4039(00)00151-9

Franzén RG. 2000. Utilization of Grignard reagents in solid-phase synthesis: A review of the literature. Tetrahedron. 56(5):685-691. https://doi.org/10.1016/S0040-4020(99)00963-1

Annila A, Lehtimäki J, Mattila K, Eriksson JE, Sivonen K, Rantala TT, Drakenberg T. 1996. Solution structure of nodularin: An inhibitor of serine/threonine- specific protein phosphatases. Journal of Biological Chemistry. 271(28):16695-16702. https://doi.org/10.1074/jbc.271.28.16695

Franzén R, Kronberg L. 1995. Synthesis of chlorinated 5-hydroxy 4-methyl-2(5H)-furanones and mucochloric acid. Tetrahedron Letters. 36(22):3905-3908. https://doi.org/10.1016/0040-4039(95)00638-S