Publications

Research Publications

This is an area dedicated to the listing of all  publications related to the TAXINOMISIS project.

Conference Publications

  1. Exarchos T, Potsika V, Mantzaris M, Fotiadis D I (2018), New concepts for the stratification of patients with carotid artery disease: Multiscale modelling and big data analytics, Biologia Serbica, BELBI 2018, Belgrade BioInformatics Conference, Belgrade, Serbia
  2. Potsika V, Mantzaris M, Siogkas P, Pappas I, Exarchos T, Fotiadis D I (2019) A multilevel approach to evaluate numerically plaque progression in carotid artery disease, 6th panhellenic conference on biomedical technology, ELEVIT, Athens, Greece
  3. Mantzaris M, Potsika V, Siogkas P, Pappas I, Exarchos T, Koncar I, Pelisek J, Andreakos E, Fotiadis D I (2019). Advanced modeling approaches and big data in a multimodal strategy for the stratification of carotid artery disease, 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Berlin, Germany
  4. Mantzaris M, Potsika V, Siogkas P, Kigka V, Pezoulas V, Pappas I, Exarchos T, Koncar I, Pelisek J, Andreakos E, Fotiadis D I (2019), A multimodal advanced approach for the stratification of carotid artery disease, 19th Annual IEEE International Conference on Bioinformatics and Bioengineering, Athens, Greece
  5. Tsakanikas V, Siogkas P, Mantzaris M, Potsika V, Kigka V, Exarchos T, Koncar I, Jovanović M, Vujčić A, Dučić S, Pelisek J, Fotiadis D I (2020). A deep learning oriented method for automated 3D reconstruction of carotid arterial trees from MR imaging, 42nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Montréal, Québec, Canada.
  6. Kigka V, Kyriakidis S, Sakellarios A, Potsika V, Tsakanikas V, Loggitsi D, Michalis L K, Fotiadis D I (2020). Three-dimensional Reconstruction of Carotid Arteries using Computed Tomography Angiography, 8th European Medical and Biological Engineering Conference, Portoroz, Slovenia
  7. Djorovic S, I. Saveljic, Filipovic N (2019). Advanced modelling approach of carotid artery atherosclerosis. 8th International Conference on Computational Bioengineering, Belgrade, Serbia
  8. Djorovic, I. Saveljic, Filipovic N (2020). Analysis of carotid plaque type based on deep learning techniques. VPH2020 Conference, Paris, France
  9. Djorovic S, I. Saveljic, Filipovic N (2020). 3D reconstruction of patient-specific carotid artery geometry using clinical ultrasound imaging. 23rd international conference on medical image computing & computer assisted intervention, Lima, Peru.
  10. Djukic T, Arsic B, Djorovic S, Filipovic N, Koncar I (2020). Validation of the machine learning approach for 3D reconstruction of carotid artery from ultrasound imaging. The 20th IEEE International Conference on BioInformatics And BioEngineering (BIBE), USA

Journal Publications

  1. Poels K, Schnitzler JG, Waissi F, Levels JHM, Stroes ESG, Daemen MJAP, Lutgens E, Pennekamp AM, De Kleijn DPV, Seijkens TTP, Kroon J. Inhibition of PFKFB3 Hampers the Progression of Atherosclerosis and Promotes Plaque Stability. Front Cell Dev Biol. 2020 Nov 12;8:581641. doi: 0.3389/fcell.2020.581641. PMID: 33282864; PMCID: PMC7688893.
  2. Dekker M, Waissi F, Timmerman N, Silvis MJM, Timmers L, de Kleijn DPV. Extracellular Vesicles in Diagnosing Chronic Coronary Syndromes the Bumpy Road to Clinical Implementation. Int J Mol Sci. 2020 Nov 30;21(23):E9128. doi: 10.3390/ijms21239128. PMID: 33266227.
  3. Timmerman N, Galyfos G, Sigala F, Thanopoulou K, de Borst GJ, Davidovic L, Eckstein HH, Filipovic N, Grugni R, Kallmayer M, de Kleijn DPV, Koncar I, Mantzaris MD, Marchal E, Matsagkas M, Mutavdzic P, Palombo D, Pasterkamp G, Potsika VT, Andreakos E, Fotiadis DI; all partners of the TAXINOMISIS Consortium. The TAXINOMISIS Project: A multidisciplinary approach for the development of a new risk stratification model for patients with asymptomatic carotid artery stenosis. Eur J Clin Invest. 2020 Dec;50(12):e13411. doi: 10.1111/eci.13411. Epub 2020 Oct 2. PMID: 32954520.
  4. Waissi F, Dekker M, Timmerman N, Hoogeveen RM, van Bennekom J, Dzobo KE, Schnitzler JG, Pasterkamp G, Grobbee DE, de Borst GJ, Stroes ESG, de Kleijn DPV, Kroon J. Elevated Lp(a)Lipoprotein[a]) Levels Increase Risk of 30-Day Major Adverse Cardiovascular Events in Patients Following Carotid Endarterectomy. Stroke. 2020 Oct;51(10):2972-2982. doi: 10.1161/STROKEAHA.120.030616. Epub 2020 Sep 3. Erratum in: Stroke. 2020 Dec;51(12):e383. PMID: 32878565.
  5. Dekker M, Waissi F, van Bennekom J, Silvis MJM, Timmerman N, Schoneveld AH, Grobbee DE, de Winter RJ, Mosterd A, Timmers L, de Kleijn DPV. Extracellular Vesicle cystatin c is associated with unstable angina in troponin negative patients with acute chest pain. PLoS One. 2020 Aug 5;15(8):e0237036. doi: 10.1371/journal.pone.0237036. PMID: 32756583; PMCID: PMC7406038.
  6. Dekker M, Waissi F, van Bennekom J, Silvis MJM, Timmerman N, Bank IEM, Walter JE, Mueller C, Schoneveld AH, Schiffelers RM, Pasterkamp G, Grobbee DE, de Winter RJ, Mosterd A, de Kleijn DPV, Timmers L. Plasma extracellular vesicle proteins are associated with stress-induced myocardial ischemia in women presenting with chest pain. Sci Rep. 2020 Jul 23;10(1):12257. doi: 10.1038/s41598-020-69297-0. PMID: 32704130; PMCID: PMC7378184.
  7. Waissi F, Dekker M, Bank IEM, Korporaal SJA, Urbanus RT, de Borst GJ, Pasterkamp G, Scholtens AM, Grobbee DE, Mosterd A, de Kleijn DPV, Timmers L. Sex differences in flow cytometry-based platelet reactivity in stable outpatients suspected of myocardial ischemia. Res Pract Thromb Haemost. 2020 May 15;4(5):879-885. doi: 10.1002/rth2.12344. PMID: 32685898; PMCID: PMC7354392.
  8. Schnitzler JG, Hoogeveen RM, Ali L, Prange KHM, Waissi F, van Weeghel M, Bachmann JC, Versloot M, Borrelli MJ, Yeang C, De Kleijn DPV, Houtkooper RH, Koschinsky ML, de Winther MPJ, Groen AK, Witztum JL, Tsimikas S, Stroes ESG, Kroon J. Atherogenic Lipoprotein(a) Increases Vascular Glycolysis, Thereby Facilitating Inflammation and Leukocyte extravasation. Circ Res. 2020 May 8;126(10):1346-1359. doi: 10.1161/CIRCRESAHA.119.316206. Epub 2020 Mar 12. PMID: 32160811; PMCID: PMC7208285.
  9. Timmerman N, de Kleijn DPV, de Borst GJ, den Ruijter HM, Asselbergs FW, Pasterkamp G, Haitjema S, van der Laan SW. Family history and polygenic risk of cardiovascular disease: Independent factors associated with secondary cardiovascular events in patients undergoing carotid endarterectomy. Atherosclerosis. 2020 Aug;307:121-129. doi: 10.1016/j.atherosclerosis.2020.04.013. Epub 2020 May 3. PMID: 32624175.
  10. Depuydt MAC, Prange KHM, Slenders L, Örd T, Elbersen D, Boltjes A, de Jager SCA, Asselbergs FW, de Borst GJ, Aavik E, Lönnberg T, Lutgens E, Glass CK, den Ruijter HM, Kaikkonen MU, Bot I, Slütter B, van der Laan SW, Yla-Herttuala S, Mokry M, Kuiper J, de Winther MPJ, Pasterkamp G. Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics. Circ Res. 2020 Nov 6;127(11):1437-1455. doi: 10.1161/CIRCRESAHA.120.316770. Epub 2020 Sep 28. PMID: 32981416; PMCID: PMC7641189.
  11. Aherrahrou R, Guo L, Nagraj VP, Aguhob A, Hinkle J, Chen L, Yuhl Soh J, Lue D, Alencar GF, Boltjes A, van der Laan SW, Farber E, Fuller D, Anane-Wae R, Akingbesote N, Manichaikul AW, Ma L, Kaikkonen MU, Björkegren JLM, Önengüt- Gümüşcü S, Pasterkamp G, Miller CL, Owens GK, Finn A, Navab M, Fogelman AM, Berliner JA, Civelek M. Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells. Circ Res. 2020 Dec 4;127(12):1552-1565. doi: 10.1161/CIRCRESAHA.120.317415. Epub 2020 Oct 12. PMID: 33040646; PMCID: PMC7718324.
  12. Mishra BH, Mishra PP, Mononen N, Hilvo M, Sievänen H, Juonala M, Laaksonen M, Hutri-Kähönen N, Viikari J, Kähönen M, Raitakari OT, Laaksonen R, Lehtimäki T. Lipidomic architecture shared by subclinical markers of osteoporosis and atherosclerosis: The Cardiovascular Risk in Young Finns Study. Bone. 2020 Feb;131:115160. doi: 10.1016/j.bone.2019.115160. Epub 2019 Nov 21.PMID: 31759205.
  13. Pashupati P. Mishra. Efficient gene set analysis of high-throughput data. From omics to pathway architecture of health and disease. https://ethesis.helsinki.fi Unigrafia Oy, Helsinki 2020.
  14. Allen NB, Krefman AE, Labarthe D, Greenland P, Juonala M, Kähönen M, Lehtimäki T, Day RS, Bazzano LA, Van Horn LV, Liu L, Alonso CF, Webber LS, Pahkala K, Laitinen TT, Raitakari OT, Lloyd-Jones DM.Cardiovascular Health Trajectories From Childhood Through Middle Age and Their Association With Subclinical Atherosclerosis. JAMA Cardiol. 2020 May 1;5(5):557-566. doi: 10.1001/jamacardio.2020.0140. PMID: 32159727
  15. Koskinen JS, Kytö V, Juonala M, Viikari JSA, Nevalainen J, Kähönen M, Lehtimäki T, Hutri-Kähönen N, Laitinen T, Tossavainen P, Jokinen E, Magnussen CG, Raitakari OT. Childhood risk factors and carotid atherosclerotic plaque in adulthood: The Cardiovascular Risk in Young Finns Study. Atherosclerosis. 2020 Jan;293:18-25. doi: 10.1016/j.atherosclerosis.2019.11.029. Epub 2019 Nov 30.PMID: 31830725.
  16. Traylor M, Amin Al Olama A, Lyytikäinen LP, Marini S, Chung J, Malik R, Dichgans M, Kähönen M, Lehtimäki T, Anderson CD, Raitakari OT, Markus HS. Influence of  Genetic Variation in PDE3A on Endothelial Function and Stroke. Hypertension. 2020 Feb;75(2):365-371.
  17.     Holvoet P, Klocke B, Vanhaverbeke M, Menten R, Sinnaeve P, Raitoharju E, Lehtimäki T,    Oksala N, Zinser C, Janssens S, Sipido K, Lyytikainen LP, Cagnin S. RNA-sequencing reveals  that STRN, ZNF484 and WNK1 add to the value of mitochondrial MT-COI and COX10 as  markers of unstable coronary artery disease. PLoS One. 2019 Dec 10;14(12):e0225621.
  18. Rinne P, Guillamat-Prats R, Rami M, Bindila L, Ring L, Lyytikäinen LP, Raitoharju E, Oksala N, Lehtimäki T, Weber C, van der Vorst EPC, Steffens S.  Palmitoylethanolamide Promotes a Proresolving Macrophage Phenotype and Attenuates Atherosclerotic Plaque Formation. Arterioscler Thromb Vasc Biol. 2018 Nov;38(11):2562-2575. doi:10.1161/ATVBAHA.118.311185. PMID: 30354245.
  19. Rinne P, Lyytikäinen LP, Raitoharju E, Kadiri JJ, Kholova I, Kähönen M, Lehtimäki T, Oksala  N. Pro-opiomelanocortin and its Processing Enzymes Associate with Plaque Stability in Human Atherosclerosis - Tampere Vascular Study. Sci Rep. 2018 Oct 10;8(1):15078. doi: 10.1038/s41598-018-33523-7. PMID: 30305673
  20. Djorovic S, Saveljic I, Filipovic N, Computational Simulation of Carotid Artery: From Patient-Specific Images to Finite Element. Analysis Journal of the Serbian Society for Computational Mechanics, 2019, ISBN 1820-6530, Vol. 13, No. 1, pp 120-129

Distinctions

  1. Virtual ESVS conference: Nathalie Timmerman received the 1st prize on the virtual ESVS conference for the presentation about the ceramides in the Taxinomisis project: “Ceramides are associated with high risk of major cardiovascular events after carotid endarterectomy”.
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This project has received funding from the
European Union’s Horizon 2020 Research and
Innovation Programme under grant agreement No
755320