1. Dmitriev R, Papkovsky D: Multi-parametric O2 Imaging in Three-Dimensional Neural Cell Models with the Phosphorescent Probes. In: Neuronal Cell Death. Edited by Lossi L, Merighi A, vol. 1254: Springer New York; 2015: 55-71. Book chapter
2. Jenkins J, Dmitriev R, Papkovsky D: Imaging Cell and Tissue O2 by TCSPC-PLIM. In: Advanced Time-Correlated Single Photon Counting Applications. Edited by Becker W, vol. 111: Springer International Publishing; 2015: 225-247. Book chapter
3. Dmitriev RI, Borisov SM, Jenkins J, Papkovsky DB: Multi-parametric imaging of tumor spheroids with ultra-bright and tunable nanoparticle O2 probes. In: Photonics West 2015: 2015. 932806-932806-932808. Published Conference proceedings (Photonics SPIE)
4. Jenkins J, Dmitriev RI, Morten K, McDermott KW, Papkovsky DB: Oxygen-sensing scaffolds for 3-dimensional cell and tissue culture. Acta Biomaterialia 2015, 16(0):126-135.
5. Dmitriev RI, Borisov SM, Düssmann H, Sun S, Müller BJ, Prehn J, Baklaushev VP, Klimant I, Papkovsky DB: Versatile Conjugated Polymer Nanoparticles for High-Resolution O2 Imaging in Cells and 3D Tissue Models. ACS Nano 2015, 9(5):5275-5288.
6. Andreev D, O'Connor P, Zhdanov A, Dmitriev R, Shatsky I, Papkovsky D, Baranov P: Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20minutes. Genome Biology 2015, 16(1):90.
7. Dmitriev RI, Papkovsky DB: Intracellular probes for imaging oxygen concentration: How good are they? Methods and Applications in Fluorescence 2015, 3(3):034001. (review)
1. Dmitriev RI, O’Donnell N, Papkovsky DB: Metallochelate Coupling of Phosphorescent Pt-Porphyrins to Peptides, Proteins, and Self-Assembling Protein Nanoparticles. Bioconjugate Chemistry 2016, 27(2):439-445.
2. Fomin M, Dmitriev RI, Jenkins J, Papkovsky DB, Heindl D, König B: A Two-Acceptor Cyanine-Based Fluorescent Indicator for NAD(P)H in Tumor Cell Models. ACS Sensors 2016, 1(6):702-709.
3. Jenkins J, Borisov SM, Papkovsky DB, Dmitriev RI: Sulforhodamine nanothermometer for multi-parametric Fluorescence Lifetime Imaging Microscopy. Analytical Chemistry 2016, 88(21):10566-10572.
4. Jenkins J, Papkovsky DB, Dmitriev RI: The Ca2+/Mn2+ -transporting SPCA2 pump is regulated by oxygen and cell density in colon cancer cells. Biochemical Journal 2016, 473(16):2507-2518.
5. Korneenko TV, Pestov NB, Ahmad N, Okkelman IA, Dmitriev RI, Shakhparonov MI, Modyanov NN: Evolutionary diversification of the BetaM interactome acquired through co-option of the ATP1B4 gene in placental mammals. Scientific Reports 2016, 6:22395.
6. Okkelman IA, Dmitriev RI, Foley T, Papkovsky DB: Use of Fluorescence Lifetime Imaging Microscopy (FLIM) as a Timer of Cell Cycle S Phase. PLOS ONE 2016, 11(12):e0167385.
7. Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G: Systematic analysis of the PTEN 5′ leader identifies a major AUU initiated proteoform. Open Biology 2016, 6(5):150203.
1. Dmitriev RI (ed.): Multi-Parametric Live Cell Microscopy of 3D Tissue Models: Springer International Publishing AG 2017; 2017. Book
2. O’Donnell N, Dmitriev RI: Three-Dimensional Tissue Models and Available Probes for Multi-Parametric Live Cell Microscopy: A Brief Overview. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models. Springer; 2017: 49-67. Book chapter
3. Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI: Multi-Parametric Imaging of Hypoxia and Cell Cycle in Intestinal Organoid Culture. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models.Springer; 2017: 85-103. Book chapter
4. Shpichka A, Koroleva A, Kuznetsova D, Dmitriev RI, Timashev P: Fabrication and Handling of 3D Scaffolds Based on Polymers and Decellularized Tissues. In: Multi-Parametric Live Cell Microscopy of 3D Tissue Models. Springer; 2017: 71-81. Book chapter
5. Okkelman IA, Foley T, Papkovsky DB, Dmitriev RI: Live cell imaging of mouse intestinal organoids reveals heterogeneity in their oxygenation. Biomaterials 2017, 146:86-96.
6. Yazgan G, Dmitriev RI, Tyagi V, Jenkins J, Rotaru G-M, Rottmar M, Rossi RM, Toncelli C, Papkovsky DB, Maniura-Weber K et al: Steering surface topographies of electrospun fibers: understanding the mechanisms. Scientific Reports 2017, 7(1):158.
1. Papkovsky D, Dmitriev R: Quenched-phosphorescence Detection of Molecular Oxygen: Applications in Life Sciences: The Royal Society of Chemistry; 2018. Book
2. Papkovsky DB, Dmitriev RI: CHAPTER 3 Evolution of Cell-penetrating Phosphorescent O2 Probes. In: Quenched-phosphorescence Detection of Molecular Oxygen: Applications in Life Sciences. Edited by Papkovsky DB, Dmitriev RI: The Royal Society of Chemistry; 2018: 50-70. Book chapter
3. Kornev VA, Grebenik EA, Solovieva AB, Dmitriev RI, Timashev PS: Hydrogel-assisted neuroregeneration approaches towards brain injury therapy: A state-of-the-art review. Computational and Structural Biotechnology Journal 2018, 16:488-502. Review
4. Papkovsky DB, Dmitriev RI: Imaging of oxygen and hypoxia in cell and tissue samples. Cell Mol Life Sci 2018, 75(16):2963-2980. Review
5. Müller BJ, Zhdanov AV, Borisov SM, Foley T, Okkelman IA, Tsytsarev V, Tang Q, Erzurumlu RS, Chen Y, Zhang H et al: Nanoparticle-Based Fluoroionophore for Analysis of Potassium Ion Dynamics in 3D Tissue Models and In Vivo. Advanced Functional Materials 2018, 28(9):1704598.
6. Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF: Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. Journal of Biological Chemistry 2018, 293:4434-4444.
7. O'Donnell N, Okkelman IA, Timashev P, Gromovykh TI, Papkovsky DB, Dmitriev RI: Cellulose-based scaffolds for fluorescence lifetime imaging-assisted tissue engineering. Acta Biomaterialia 2018, 80:85-96.
1. Dalfen I, Dmitriev RI, Holst G, Klimant I, Borisov SM: Background-Free Fluorescence-Decay-Time Sensing and Imaging of pH with Highly Photostable Diazaoxotriangulenium Dyes. Analytical Chemistry 2019, 91(1):808-816.
2. Grebenik EA, Istranov LP, Istranova EV, Churbanov SN, Shavkuta BS, Dmitriev RI, Veryasova NN, Kotova SL, Kurkov AV, Shekhter AB et al: Chemical cross-linking of xenopericardial biomeshes: A bottom-up study of structural and functional correlations. Xenotransplantation 2019, 0(0):e12506.
3. Koren K, Gravesen Salinas NK, Santella M, Moßhammer M, Müller M-C, Dmitriev RI, Borisov SM, Kühl M, Laursen BW: Evaluation of Ebselen-azadioxatriangulenium as redox-sensitive fluorescent intracellular probe and as indicator within a planar redox optode. Dyes and Pigments 2019:107866.
4. Okkelman IA, Papkovsky DB, Dmitriev RI: Estimation of the Mitochondrial Membrane Potential Using Fluorescence Lifetime Imaging Microscopy. Cytometry Part A 2019, 0(0).
1. Okkelman IA, Neto N, Papkovsky DB, Monaghan MG, Dmitriev RI: A deeper understanding of intestinal organoid metabolism revealed by combining fluorescence lifetime imaging microscopy (FLIM) and extracellular flux analyses. Redox Biology 2020, 30:101420.
2. Elagin V, Kuznetsova D, Grebenik E, Zolotov DA, Istranov L, Zharikova T, Istranova E, Polozova A, Reunov D, Kurkov A et al: Multiparametric Optical Bioimaging Reveals the Fate of Epoxy Crosslinked Biomeshes in the Mouse Subcutaneous Implantation Model. Frontiers in Bioengineering and Biotechnology 2020, 8(107).
3. Neto N, Dmitriev RI, Monaghan MG: Seeing Is Believing: Noninvasive Microscopic Imaging Modalities for Tissue Engineering and Regenerative Medicine. In: Cell Engineering and Regeneration. Edited by Gimble JM, Marolt Presen D, Oreffo R, Redl H, Wolbank S. Cham: Springer International Publishing; 2020: 1-41.
4. Kawashima M, Bensaad K, Zois CE, Barberis A, Bridges E, Wigfield S, Lagerholm C, Dmitriev RI, Tokiwa M, Toi M et al: Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells. Cancer & Metabolism 2020, 8(1):13.
5. Okkelman IA, Puschhof J, Papkovsky DB, Dmitriev RI: Visualization of Stem Cell Niche by Fluorescence Lifetime Imaging Microscopy. In: Intestinal Stem Cells: Methods and Protocols. Edited by Ordóñez-Morán P. New York, NY: Springer US; 2020: 65-97.
After joining Ghent University:
6. Okkelman I, McGarrigle R, O'Carroll S, Carvajal Berrio D, Schenke-Layland K, Hynes J, Dmitriev RI: Extracellular Ca2+-sensing fluorescent protein biosensor based on a collagen-binding domain. ACS Applied Bio Materials 2020.
Perottoni S, Neto NGB, Di Nitto C, Dmitriev RI, Raimondi MT, Monaghan MG: Intracellular label-free detection of mesenchymal stem cell metabolism within a perivascular niche-on-a-chip. Lab on a Chip 2021, 21(7):1395-1408.
Dmitriev RI, Intes X, Barroso M: Luminescence lifetime imaging of three-dimensional biological objects. Review. Journal of Cell Science 2021, 134(9): 1-17.
Peirsman A, Blondeel E, Ahmed T, Anckaert J, Audenaert D, Boterberg T, Buzas K, Carragher N, Castellani G, Castro F: MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity. Nature methods 2021:1-10.
Okkelman IA, Vercruysse C, Kondrashina AV, Borisov SM, Dmitriev RI: Affordable Oxygen Microscopy-Assisted Biofabrication of Multicellular Spheroids. JoVE 2022:e63403.
Van de Voorde B, Sensu B, De Vos L, Colenbier R, Baskan H, Geltmeyer J, Parmentier L, Van Daele L, Dmitriev RI, Pyl L et al: Electrospinning of poly(decamethylene terephthalate) to support vascular graft applications. European Polymer Journal 2022:111003.
Debruyne AC, Okkelman IA, Dmitriev RI: Balance between the cell viability and death in 3D (review). Seminars in Cell & Developmental Biology 2022. https://doi.org/10.1016/j.semcdb.2022.09.005
Russegger A, Debruyne AC, Berrio DC, Fuchs S, Marzi J, Schenke-Layland K, Dmitriev RI, Borisov SM: Bright and Photostable TADF-Emitting Zirconium(IV) Pyridinedipyrrolide Complexes: Efficient Dyes for Decay Time-Based Temperature Sensing and Imaging. Advanced Optical Materials 2023, n/a(n/a):2202720.
Okkelman IA, Dmitriev RI: Fluorescence Intensity and Fluorescence Lifetime Imaging Microscopies (FLIM) of Cell Differentiation in the Small Intestinal Organoids Using Cholera Toxin. In: Intestinal Differentiated Cells: Methods and Protocols. Edited by Ordóñez-Morán P. New York, NY: Springer US; 2023: 171-195.
Van Daele L, Van de Voorde B, Colenbier R, De Vos L, Parmentier L, Van der Meeren L, Skirtach A, Dmitriev RI, Dubruel P, Van Vlierberghe S: Effect of molar mass and alkyl chain length on the surface properties and biocompatibility of poly(alkylene terephthalate)s for potential cardiovascular applications. Journal of Materials Chemistry B 2023.
Parmentier L, D'Haese S, Carpentier N, Dmitriev RI, Van Vlierberghe S: Bottom-up Extrusion-Based Biofabrication of the Osteoid Niche. Macromolecular Bioscience 2023, n/a(n/a):2300395.
Parmentier L, D'Haese S, Duquesne J, Bray F, Van der Meeren L, Skirtach AG, Rolando C, Dmitriev RI, Van Vlierberghe S: 2D fibrillar osteoid niche mimicry through inclusion of visco-elastic and topographical cues in gelatin-based networks. International Journal of Biological Macromolecules 2023:127619.
Barroso M, Monaghan MG, Niesner R, Dmitriev RI: Probing organoid metabolism using fluorescence lifetime imaging microscopy (FLIM): The next frontier of drug discovery and disease understanding. Advanced Drug Delivery Reviews 2023, 201:115081.
Cruyssen RVd, Devan J, Heggli I, Burri D, Gaublomme D, Josipovic I, Dumas E, Vlieghe C, Raimondo MG, Zakharov P et al: GDF15 mediates inflammation-associated bone loss through a brain-bone axis. bioRxiv 2023:2023.2011.2022.568290. (PREPRINT)
Debruyne AC, Okkelman IA, Heymans N, Nobis M, Borisov SM, Dmitriev RI: Live microscopy of multicellular spheroids with the multi-modal near-infrared nanoparticles reveals differences in oxygenation gradients. bioRxiv 2023:2023.2012.2011.571110. (PREPRINT, published in revised form in ACS Nano in 2024)
Barra J, Crosbourne I, Roberge CL, Bossardi-Ramos R, Warren JSA, Matteson K, Wang L, Jourd’heuil F, Borisov SM, Bresnahan E et al: DMT1-dependent endosome-mitochondria interactions regulate mitochondrial iron translocation and metastatic outgrowth. Oncogene 2024. https://www.nature.com/articles/s41388-023-02933-x
Russegger A, Fischer SM, Debruyne AC, Wiltsche H, Boese AD, Dmitriev RI, Borisov SM: Tunable Self-Referenced Molecular Thermometers via Manipulation of Dual Emission in Platinum(II) Pyridinedipyrrolide Complexes. ACS Applied Materials & Interfaces 2024.
Debruyne AC, Okkelman IA, Heymans N, Pinheiro C, Hendrix A, Nobis M, Borisov SM, Dmitriev RI: Live Microscopy of Multicellular Spheroids with the Multimodal Near-Infrared Nanoparticles Reveals Differences in Oxygenation Gradients. ACS Nano 2024, 18(19):12168-12186.
Debruyne AC, Ferrari G, Zhou H, Van Loon N, Heymans N, Okkelman IA, Dmitriev RI: Production and Multi-Parameter Live Cell Fluorescence Lifetime Imaging Microscopy (FLIM) of Multicellular Spheroids. JoVE 2024(210):e66845.
Billiet L, Jansen H, Pille M, Boehme L, Sanchez Sanchez G, De Cock L, Goetgeluk G, Pascal E, De Munter S, Deseins L et al: ThymoSpheres culture: A model to study human polyclonal unconventional T cells. European Journal of Immunology 2024, n/a(n/a):2451265.
Parmentier L, D‘Haese S, Van der Meeren L, Szabó A, Skirtach AG, Dmitriev RI, Locs J, Van Vlierberghe S: Mimicking the Bone Extracellular Matrix through a Calcium Phosphate-Containing Thiol–Ene Cross-Linked Gelatin Composite. Biomacromolecules 2024.
Sheehan A, Okkelman IA, Groslambert G, Bucher C, Dmitriev RI, Filatov MA: Optoelectronic Properties and Fluorescence Lifetime Imaging Application of Donor-Acceptor Dyads Derived From 2,6-DicarboxyBODIPY. Chemistry – A European Journal 2024, n/a(n/a):e202404188. (accepted 31-Dec-2024)
Duquesne J, Parmentier L, Vermeersch E, Lemaire F, Won Seo J, Dmitriev RI, Van Vlierberghe S: Volumetric bioprinting of the osteoid niche. Biofabrication 2025.
Sommers V, David K, Helsen C, Moermans K, Stockmans I, Ferrari G, Dmitriev R, Stegen S, Meijer OC, Kroon J et al: Androgens differentially modulate glucocorticoid effects on adipose tissue and lean mass. Journal of Endocrinology 2025:JOE-24-0061.
Vanhoeijen R, Okkelman IA, Rogier N, Sedlačík T, Stöbener DD, Devriendt B, Dmitriev RI, Hoogenboom R: Poly(2-alkyl-2-oxazoline) Hydrogels as Synthetic Matrices for Multicellular Spheroid and Intestinal Organoid Cultures. Biomacromolecules 2025.
Vanhove L, Van Gansbeke T, Devriendt B, Van der Meeren R, Dmitriev RI, Okkelman IA: Lack of biochemical signalling in GelMA leads to polarity reversion in intestinal organoids independent from mechanoreciprocity. Journal of Tissue Engineering 2025, 16:20417314251345000.
Okkelman IA, Zhou H, Borisov SM, Debruyne AC, Lefebvre AEYT, Leomil Zoccoler M, Chen L, Devriendt B, Dmitriev RI: Visualizing the internalization and biological impact of nanoplastics in live intestinal organoids by Fluorescence Lifetime Imaging Microscopy (FLIM). Light: Science & Applications 2025, 14(1):272.
Chen L, Van Der Weken H, Zwaenepoel O, Okkelman IA, Aelvoet J, Van Denberghe E, Gettemans J, Dmitriev RI, De Geest BG, Cox E et al: Cell-specific mRNA delivery via nanobody-functionalized lipid nanoparticles. Journal of Controlled Release 2025, 388:114365.