Research output per year
Research output per year
Publications
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2024
An imaging scheme to study the flow dynamics of co-flow regimes in microfluidics: implications for nanoprecipitation
Inam, W., Vladyka, A., Pylvänäinen, J., Solis, J., Tokic, D., Kankaanpää, P. & Zhang, H., 31 Oct 2024, (E-pub ahead of print) In: Lab on a Chip.Research output: Contribution to journal › Article › Scientific › peer-review
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Apprehensions and emerging solutions in ML-based protein structure prediction
Dahlström, K. M. & Salminen, T. A., Jun 2024, In: Current Opinion in Structural Biology. 86, 102819.Research output: Contribution to journal › Review Article or Literature Review › peer-review
Open AccessFile3 Citations (Scopus)17 Downloads (Pure) -
A step towards tuning the jute fiber structure and properties by employing sodium periodate oxidation and coating with alginate
Ivanovska, A., Milosevic, M., Ladarevic, J., Jankoska, M., Matic, T., Svircev, Z. & Kostic, M., Feb 2024, In: International Journal of Biological Macromolecules. 257, 11 p., 128668.Research output: Contribution to journal › Article › Scientific › peer-review
6 Citations (Scopus) -
Bioimage Analysis for Life Scientists: Tools for Live Cell Imaging
Pylvänäinen, J., 26 Apr 2024, Åbo: Åbo Akademi.Research output: Types of Thesis › Doctoral Thesis › Collection of Articles
Open Access -
Body‐wide genetic deficiency of poly(ADP‐ribose) polymerase 14 sensitizes mice to colitis
Vedantham, M., Polari, L., Poosakkannu, A., Pinto, R. G., Sakari, M., Laine, J., Sipilä, P., Määttä, J., Gerke, H., Rissanen, T., Rantakari, P., Toivola, D. M. & Pulliainen, A. T., 15 Jul 2024, In: FASEB Journal. 38, 13, 23 p., e23775.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile3 Downloads (Pure) -
Building shape-focused pharmacophore models for effective docking screening
Moyano-Gómez, P., Lehtonen, J., Pentikäinen, O. & Postila, P., Dec 2024, In: Journal of Cheminformatics. 16, 1, p. 97 1.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)7 Downloads (Pure) -
CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data
Gómez-de-Mariscal, E., Grobe, H., Pylvänäinen, J. W., Xénard, L., Henriques, R., Tinevez, J.-Y. & Jacquemet, G., 8 Aug 2024, In: PLoS Biology. 22, 8, 19 p., e3002740.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile8 Downloads (Pure) -
Characterization of cyanobacterial mats from an artificial hot spring in Uniejów (Poland) and the potential use of their biomass
Rybak, A. S., Dziuba, M., Pełechata, A., Rybak, M., Akter, S., Czerepska, A., Dulić, T., Gąbka, M., Hindáková, A., Jurczak, T., Kendir, A., Mankiewicz-Boczek, J., Meriluoto, J. & Wejnerowski, Ł., Aug 2024, In: Algal Research. 82, 41 p., 103646.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
Characterization of Immune Cell Populations of Cutaneous Neurofibromas in Neurofibromatosis 1
Kallionpää, R. A., Peltonen, S., Le, K. M., Martikkala, E., Jääskeläinen, M., Fazeli, E., Riihilä, P., Haapaniemi, P., Rokka, A., Salmi, M., Leivo, I. & Peltonen, J., Jan 2024, In: Laboratory Investigation. 104, 1, p. 100285 100285.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)19 Downloads (Pure) -
Community Structure and Toxicity Potential of Cyanobacteria during Summer and Winter in a Temperate-Zone Lake Susceptible to Phytoplankton Blooms
Wejnerowski, Ł., Dulić, T., Akter, S., Font-Nájera, A., Rybak, M., Kamiński, O., Czerepska, A., Dziuba, M. K., Jurczak, T., Meriluoto, J., Mankiewicz-Boczek, J. & Kokociński, M., Aug 2024, In: Toxins. 16, 8, 357.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile11 Downloads (Pure) -
Defining a timeline of colon pathologies after keratin 8 loss: Rapid crypt elongation and diarrhea are followed by epithelial erosion and cell exfoliation
Ilomäki, M., Polari, L., Stenvall, C.-G. A., Tayyab, M., Kähärä, K., Ridge, K. M. & Toivola, D. M., 1 Jan 2024, In: AJP - Gastrointestinal and Liver Physiology. 326, 1, p. G67-G77 11 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile2 Citations (Scopus)112 Downloads (Pure) -
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible
AI4Life Horizon Europe Program Consortium, Jun 2024, In: Nature Methods. 21, 6, p. 925-927 3 p.Research output: Contribution to journal › Article › Scientific
1 Citation (Scopus) -
DLL4/Notch3/WNT5B axis mediates bidirectional prometastatic crosstalk between melanoma and lymphatic endothelial cells
Alve, S., Gramolelli, S., Jukonen, J., Juteau, S., Pink, A., Manninen, A. A., Hänninen, S., Monto, E., Lackman, M. H., Carpén, O., Saharinen, P., Karaman, S., Vaahtomeri, K. & Ojala, P. M., 9 Jan 2024, In: JCI Insight. 9, 1, 21 p., e171821.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)10 Downloads (Pure) -
Estrogen deprivation and estrogen receptor α antagonism decrease DSS colitis in female mice
Hjelt, A., Anttila, S., Wiklund, A., Rokka, A., Al‐Ramahi, D., Toivola, D. M., Polari, L. & Määttä, J., Aug 2024, In: Pharmacology Research & Perspectives. 12, 4, 16 p., e1234.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
Evaluation of bone marrow glucose uptake and adiposity in male rats after diet and exercise interventions
Ojala, R., Widjaja, N., Hentilä, J., Jalo, A., Helin, J. S., Nissinen, T. A., Jalava, N., Eskola, O., Rajander, J., Löyttyniemi, E., Ivaska, K. K. & Hannukainen, J. C., 14 Jun 2024, In: Frontiers in Endocrinology. 15, 1422869.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile -
Exogenous Trehalose Improves Growth, Glycogen and Poly-3-Hydroxybutyrate (PHB) Contents in Photoautotrophically Grown Arthrospira platensis under Nitrogen Deprivation.
Mudtham, N.-A., Promariya, A., Duangsri, C., Maneeruttanarungroj, C., Ngamkala, S., Akrimajirachoote, N., Powtongsook, S., Salminen, T. A. & Raksajit, W., 18 Feb 2024, In: Biology. 13, 2, 127.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Downloads (Pure) -
Germline-specific RNA helicase DDX4 forms cytoplasmic granules in cancer cells and promotes tumor growth
Olotu, O., Koskenniemi, A.-R., Ma, L., Paramonov, V., Laasanen, S., Louramo, E., Bourgery, M., Lehtiniemi, T., Laasanen, S., Rivero-Müller, A., Löyttyniemi, E., Sahlgren, C., Westermarck, J., Ventelä, S., Visakorpi, T., Poutanen, M., Vainio, P., Mäkelä, J.-A. & Kotaja, N., 23 Jul 2024, In: Cell Reports. 43, 7, 32 p., 114430.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile8 Downloads (Pure) -
Glial reactivity in a mouse model of beta-amyloid deposition assessed by PET imaging of P2X7 receptor and TSPO using [11C]SMW139 and [18F]F-DPA
Alzghool, O. M., Aarnio, R., Helin, J. S., Wahlroos, S., Keller, T., Matilainen, M., Solis, J., . Danon, J. J., Kassiou, M., Snellman, A., Solin, O., Rinne, J. O. & Haaparanta-Solin, M., 6 Mar 2024, In: EJNMMI Research. 14, 25, 25.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile2 Citations (Scopus)8 Downloads (Pure) -
Glutaraldehyde-enhanced autofluorescence as a general tool for 3D morphological imaging
Niemeläinen, M., Haapanen-Saaristo, A.-M., Koskinen, L. M., Gullmets, J., Peuhu, E., Meinander, A., Calhim, S. & Paatero, I., 15 Nov 2024, In: Biology Open. 13, 11Research output: Contribution to journal › Article › Scientific › peer-review
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Harnessing artificial intelligence to reduce phototoxicity in live imaging
Gómez-de-Mariscal, E., Del Rosario, M., Pylvänäinen, J. W., Jacquemet, G. & Henriques, R., 1 Feb 2024, In: Journal of Cell Science. 137, 3Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)13 Downloads (Pure) -
Imaging cell architecture and dynamics
Collinson, L. & Jacquemet, G., 15 Oct 2024, In: Journal of Cell Science.Research output: Contribution to journal › Article › Scientific
Open Access -
Improved breast milk proteome coverage by DIA based LC-MS/MS method
Viitaharju, J., Polari, L., Kauko, O., Merilahti, J., Rokka, A., Toivola, D. M. & Laitinen, K., Jul 2024, In: Proteomics. 24, 14, 2300340.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)10 Downloads (Pure) -
Menetelmiä ja työkaluja lineaaristen ubikitiiniketjujen tunnistamiseen syöpäsoluissa ja suolistossa
Luukkonen, V., 12 Jul 2024, In: Solubiologi. 1, p. 12-15 4 p.Research output: Contribution to journal › Article › Professional
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Particulate air pollution in Central Serbia and some proposed measures for the restoration of degraded and disturbed mining areas
Mihalj, I., Šušak, S., Palanački-Malešević, T., Važić, T., Jurca, T., Pavić, D., Simeunović, J., Vulin, A., Meriluoto, J. & Svirčev, Z., Sept 2024, In: Geographica Pannonica. 28, 3, p. 205-220 16 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile3 Downloads (Pure) -
Restoration of damaged drylands through acceleration of biocrust development
Palanački Malešević, T., Meriluoto, J., Mihalj, I., Vazic, T., Markovic, R., Jurca, T., Svircev, Z., Codd, G. A. & Svircev, Z., Sept 2024, In: CATENA. 244, 108265.Research output: Contribution to journal › Review Article or Literature Review › peer-review
1 Citation (Scopus) -
SHANK3 depletion leads to ERK signalling overdose and cell death in KRAS-mutant cancers
Lilja, J., Kaivola, J., Conway, J. R. W., Vuorio, J., Parkkola, H., Roivas, P., Dibus, M., Chastney, M. R., Varila, T., Jacquemet, G., Peuhu, E., Wang, E., Pentikäinen, U., Posada, I. M. D., Hamidi, H., Najumudeen, A. K., Sansom, O. J., Barsukov, I. L., Abankwa, D. & Vattulainen, I. & 2 others, , Dec 2024, In: Nature Communications. 15, 1, 8002.Research output: Contribution to journal › Article › Scientific › peer-review
Open Access1 Citation (Scopus) -
Signaling downstream of tumor-stroma interaction regulates mucinous colorectal adenocarcinoma apicobasal polarity
Pasquier, N., Isomursu, A., Hamidi, H., Mathieu, J. R. R., Härkönen, J., Follain, G., Desterke, C., Fusilier, Z., Solis, J., Belaya, I., Kankaanpää, P., Barresi, V., Cartry, J., Bedja, S., Jaulin, F. & Ivaska, J., 21 Nov 2024, (Accepted/In press).Research output: Working paper › Preprint
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Structural Catalytic Core in Subtilisin-like Proteins and Its Comparison to Trypsin-like Serine Proteases and Alpha/Beta-Hydrolases
Denesyuk, A., Denessiouk, K., Johnson, M. & Uversky, V., 2024, In: International Journal of Molecular Sciences. 25, 22, p. 11858Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Structural Catalytic Core of the Members of the Superfamily of Acid Proteases
Denesyuk, A., Denessiouk, K., Johnson, M. & Uversky, V., 2024, In: Molecules. 29, 15, p. 3451Research output: Contribution to journal › Article › Scientific › peer-review
Open Access -
Surface Modification of Mesoporous Silica Nanoparticles as a Means to Introduce Inherent Cancer-Targeting Ability in a 3D Tumor Microenvironment
Prabhakar, N., Långbacka, E., Özliseli, E., Mattsson, J., Mahran, A., Suleymanova, I., Sahlgren, C., Rosenholm, J., Åkerfelt, M. & Nees, M., Sept 2024, In: Small Science. 4, 9, 12 p., 2400084.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)15 Downloads (Pure) -
Taide Kohtaa Tieteen: Forcing the Impossible-Hanke ja Tieteen yhteiskunnallinen vaikuttavuus
Hellsten, L., Weckman, J.-K., Jacquemet, G., Ringbom, A., Runeberg, R., Andersson, J.-E., Huynh, T. P., Fogde, A., Raar, M., Custódio, L., Långbacka, U., Mastovaara, T., Kyytinen, T. & Berger, F., 2024, (Submitted) In: Nykykulttuuri-Julkaisusarja.Research output: Contribution to journal › Article › Professional
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The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc- Oxy) and Acid–Base zones
Denessiouk, K., Denesyuk, A., Permyakov, S. E., Permyakov, E. A., Johnson, M. & Uversky, V. N., Jan 2024, In: Current Research in Structural Biology. 7, 9 p., 100123.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)101 Downloads (Pure) -
The keratin-desmosome scaffold of internal epithelia in health and disease - The plot is thickening
Toivola, D. M., Polari, L., Schwerd, T., Schlegel, N. & Strnad, P., Feb 2024, In: Current Opinion in Cell Biology. 86, 8 p., 102282.Research output: Contribution to journal › Review Article or Literature Review › peer-review
Open AccessFile2 Citations (Scopus)68 Downloads (Pure) -
TLNRD1 is a CCM complex component and regulates endothelial barrier integrity
Ball, N. J., Ghimire, S., Follain, G., Pajari, A. O., Wurzinger, D., Vaitkevičiūtė, M., Cowell, A. R., Berki, B., Ivaska, J., Paatero, I., Goult, B. T. & Jacquemet, G., 2 Sept 2024, In: Journal of Cell Biology. 223, 9, 22 p., e202310030.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile8 Downloads (Pure) -
Trans-activating mutations of the pseudokinase ERBB3
Koivu, M., Chakroborty, D., Airenne, T., Johnson, M., Kurppa, K. & Elenius, K., 12 Jul 2024, In: Oncogene. 43, 29, p. 2253-2265 43(29).Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile2 Citations (Scopus)5 Downloads (Pure) -
Two groups and three classes of the conserved structural organization of nucleophile and non-canonical ElbowFlankOxy networks in different superfamily proteins
Denessiouk, K., Denesyuk, A., Johnson, M. & Uversky, V., 2024, In: Journal of Biomolecular Structure and Dynamics. 15, p. 1-16Research output: Contribution to journal › Article › Scientific › peer-review
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Ubiquitin signalling in Drosophila innate immune responses
Aalto, A., Luukkonen, V. & Meinander, A., 16 Oct 2024, In: FEBS Journal. 291, 20, p. 4397-4413Research output: Contribution to journal › Review Article or Literature Review › peer-review
Open AccessFile1 Citation (Scopus)29 Downloads (Pure) -
Vascular Cells and Mechanical Signals: A study of the role of Jagged1 in vascular mechanosensing
Suarez Rodriguez, F., 17 Dec 2024, Åbo: Åbo Akademi.Research output: Types of Thesis › Doctoral Thesis › Collection of Articles
Open Access -
Vimentin at the core of wound healing
Coelho-Rato, L. S., Parvanian, S., Modi, M. K. & Eriksson, J. E., Mar 2024, In: Trends in Cell Biology. 34, 3, p. 239-254 16 p.Research output: Contribution to journal › Review Article or Literature Review › peer-review
9 Citations (Scopus) -
2023
A multiscale computational model of arterial growth and remodeling including Notch signaling
van Asten, J. G. M., Latorre, M., Karakaya, C., Baaijens, F. P. T., Sahlgren, C. M., Ristori, T., Humphrey, J. D. & Loerakker, S., Oct 2023, In: Biomechanics and modeling in mechanobiology. 22, 5, p. 1569-1588Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile5 Citations (Scopus)44 Downloads (Pure) -
An in vitro model of cancer invasion with heterogeneous ECM created with droplet microfluidics
Jouybar, M., Sleeboom, J., Vaezzadeh, E., Sahlgren, C. & den Toonder, J., 23 Nov 2023, In: Frontiers in Bioengineering and Biotechnology. 11, 16 p., 1267021.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile1 Citation (Scopus)18 Downloads (Pure) -
Calcium Signaling in Cell Compartments – the Importance of Sphingosine Kinase 1 and ORP5/8
Pulli, I., 2023, Åbo: Åbo Akademi.Research output: Types of Thesis › Doctoral Thesis › Collection of Articles
Open Access -
Cancer cell invasion alters the protein profile of extracellular vesicles
Luoto, J. C., Coelho‐Rato, L. S., Jungarå, C., Bengs, S. H., Roininen, J., Eriksson, J. E., Sistonen, L. & Henriksson, E., Dec 2023, In: Journal of Extracellular Biology. 2, 12, 15 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile35 Downloads (Pure) -
Comprehensive characterization of the embryonic factor LEUTX
Gawriyski, L., Jouhilahti, E.-M., Yoshihara, M., Fei, L., Weltner, J., Airenne, T. T., Trokovic, R., Bhagat, S., Tervaniemi, M. H., Murakawa, Y., Salokas, K., Liu, X., Miettinen, S., Bürglin, T. R., Sahu, B., Otonkoski, T., Johnson, M. S., Katayama, S., Varjosalo, M. & Kere, J., 17 Mar 2023, In: iScience. 26, 3, 29 p., 106172.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile8 Citations (Scopus)19 Downloads (Pure) -
Defined extracellular matrix compositions support stiffness-insensitive cell spreading and adhesion signaling
Conway, J. R. W., Isomursu, A., Follain, G., Härmä, V., Jou-Ollé, E., Pasquier, N., Välimäki, E. P. O., Rantala, J. K. & Ivaska, J., 24 Oct 2023, In: Proceedings of the National Academy of Sciences of the United States of America. 120, 43, 10 p., e2304288120.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile7 Citations (Scopus)34 Downloads (Pure) -
Detection of Intestinal Inflammation by Vascular Adhesion Protein-1-Targeted [68Ga]Ga-DOTA-Siglec-9 Positron Emission Tomography in Murine Models of Inflammatory Bowel Disease
Bhowmik, A. A., Heikkilä, T. R. H., Polari, L., Virta, J., Liljenbäck, H., Moisio, O., Li, X.-G., Viitanen, R., Jalkanen, S., Koffert, J., Toivola, D. M. & Roivainen, A., 18 Dec 2023, (E-pub ahead of print) In: Molecular Imaging and Biology. 12 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile13 Downloads (Pure) -
Environmental stiffness restores mechanical homeostasis in vimentin-depleted cells
Grolleman, J., van Engeland, N. C. A., Raza, M., Azimi, S., Conte, V., Sahlgren, C. M. & Bouten, C. V. C., 26 Oct 2023, In: Scientific Reports. 13, 12 p., 18374.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile3 Citations (Scopus)30 Downloads (Pure) -
Fast4DReg - fast registration of 4D microscopy datasets
Pylvänäinen, J. W., Laine, R. F., Saraiva, B. M. S., Ghimire, S., Follain, G., Henriques, R. & Jacquemet, G., 15 Feb 2023, In: Journal of Cell Science. 136, 4Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile4 Citations (Scopus)31 Downloads (Pure) -
Fast4DReg – to the rescue of your drifty microscopy data
Pylvänäinen, J., 13 Mar 2023, The Company of Biologists.Research output: Other contribution › Blog article › Professional
Open Access -
High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation
Laine, R. F., Heil, H. S., Coelho, S., Nixon-Abell, J., Jimenez, A., Wiesner, T., Martínez, D., Galgani, T., Régnier, L., Stubb, A., Follain, G., Webster, S., Goyette, J., Dauphin, A., Salles, A., Culley, S., Jacquemet, G., Hajj, B., Leterrier, C. & Henriques, R., Dec 2023, In: Nature Methods. 20, 12, p. 1949-1956 25 p.Research output: Contribution to journal › Article › Scientific › peer-review
Open AccessFile19 Citations (Scopus)31 Downloads (Pure)