Publications

Peer-reviewed Publications

 
See my publications profile in:  PubMed || Scopus || ORCID || Google Scholar || Microsoft Academic || ResearchGate || Publons || Academia.edu

PREPRINTS

  1. Karatzas, E., Baltoumas, F.A., Aplakidou, E., Kontou, P.I., Stathopoulos, P., Stefanis, L., Bagos, P.G., Pavlopoulos, G.A. (2023) Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources. bioRxiv 2023.02.21.529389; doi: 10.1101/2023.02.21.529389.
  2. Tzaferis, C., Karatzas, E., Baltoumas, F.A., Pavlopoulos, G.A., Kollias, G., Konstantopoulos, D. (2022) SCALA: A web application for multimodal analysis of single cell next generation sequencing data. bioRxiv 2022.11.24.517826; doi: 10.1101/2022.11.24.517826
  3. Kokoli, M., Karatzas, E., Baltoumas, F.A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, N.T., Jensen, L.J., Pavlopoulos, G.A. (2022) Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. bioRxiv 2022.10.01.510435. doi: 10.1101/2022.10.01.510435

PUBLISHED

  1. Baltoumas, F.A., Karatzas, E., Paez-Espino, D., Venetsianou, N.K., Aplakidou, E., Oulas, A., Finn, R.D., Ovchinnikov, S., Pafilis, E., Kyrpides, N.C., Pavlopoulos, G.A. (2023) Exploring microbial functional biodiversity at the protein family level – from metagenomic sequence reads to annotated protein clusters. Frontiers in Bioinformatics, 2023, Vol. 3; doi: 10.3389/fbinf.2023.1157956.
  2. Filis, G., Baltoumas, F.A., Spanogiannis, G., Litou, Z.I., Iconomidou, V.A. (2023) Proteome-Wide Detection and Annotation of Receptor Tyrosine Kinases (RTKs): RTK-PRED and the TyReK Database. Biomolecules, 2023, 13(2), 270, doi: 10.3390/biom13020270.
  3. Baltoumas, F.A., Sofras, D., Apostolakou, A.E., Litou, Z.I., Iconomidou, V.A. (2023) NucEnvDB: A Database of Nuclear Envelope Proteins and Their Interactions. Membranes, 2023; 13, 62, doi: 10.3390/membranes13010062.
  4. Karatzas, E., Koutrouli, M., Baltoumas, F., Papanikolopoulou, K., Bouyioukos, C.,  Pavlopoulos, G.A. (2022) The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies. Bioinformatics Advances, vbac036. doi: 10.1093/bioadv/vbac036.
  5. Karatzas, E., Baltoumas, F.A., Kasionis, I., Sanoudou, D., Eliopoulos, A.G., Theodosiou, T., Iliopoulos, I., Pavlopoulos, G.A. (2022) Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining. Biomolecules. 2022; 12(4):520. doi: 10.3390/biom12040520.
  6. Baltoumas, F.A., Zafeiropoulou, S., Karatzas, E., Paragkamian, S., Thanati, F., Iliopoulos, I., Eliopoulos, A.G., Schneider, R., Jensen, L.J., Pafilis, E., Pavlopoulos, G.A. (2021) OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. NAR Genomics and Bioinformatics, 2021, Vol. 3, No. 4. doi: 10.1093/nargab/lqab090.
  7. Baltoumas, F.A., Zafeiropoulou, S., Karatzas, E., Koutrouli, M., Thanati, F., Voutsadaki, K., Gkonta, M., Hotova, J., Kasionis, I., Hatzis, P., Pavlopoulos, G.A. (2021) Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. Biomolecules, 11(8):1245. doi: 10.3390/biom11081245.
  8. Thanati, F., Karatzas, E., Baltoumas, F.A., Stravopodis, D.J., Eliopoulos, A.G., Pavlopoulos, G.A. (2021) FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists. Biology (Basel). Jul 14;10(7):665. doi: 10.3390/biology10070665.
  9. Karatzas, E., Gkonta, M., Hotova, J., Baltoumas, F.A., Kontou, P.I., Bobotsis, C.J., Bagos, P.G., Pavlopoulos, G.A. (2021) VICTOR: A visual analytics web application for comparing cluster sets. Computers in Biology & Medicine, Vol. 135, Aug. 2021, 104557. doi: 10.1016/j.compbiomed.2021.104557.
  10. Karatzas, E., Baltoumas, F.A., Panayiotou, N.A., Schneider, R., Pavlopoulos, G.A. (2021) Arena3Dweb: Interactive 3D visualization of multilayered networks. Nucleic Acids Res. 2021 Apr 22;gkab278. doi: 10.1093/nar/gkab278.
  11. Apostolakou, A.E., Baltoumas, F.A., Stravopodis, D.J., Iconomidou, V.A. (2020) Extended Human GPCR Network (hGPCRnet): Cell-Type-Specific Analysis of GPCR Signaling Pathways. J. Proteome Res. 19 (1), 511-524. doi: 10.1021/acs.jproteome.9b00754.
  12. Tsiolaki, P.L., Nasi, G.I., Baltoumas, F.A., Fishman, S., Tu, H.S., Iconomidou, V.A. (2019) Delving into the Amyloidogenic Core of Human Leukocyte Chemotactic Factor 2 . J. Struct. Biol. 207(3):260-269. doi: 10.1016/j.jsb.2019.06.001.
  13. Baltoumas, F.A., Hamodrakas, S.J., Iconomidou V.A. (2019) The Gram-Negative Outer Membrane Modeler: automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields. J. Comput. Chem. Jul 5; 40(18): 1727-1734. doi: 10.1002/jcc.25823.
  14. Tsiolaki, P.L., Katsafana, A.D., Baltoumas, F.A., Louros, N.N., Iconomidou, V.A. (2019) Hidden Aggregation Hot-Spots on Human Apolipoprotein E: A Structural Study. Int. J. Mol. Sci. 20(9):E2274. doi: 10.3390/ijms20092274.
  15. Triantaphyllopoulos, K.A., Baltoumas, F.A. & Hamodrakas, S.J. (2019) Structural Characterization and Molecular Dynamics simulations of the caprine and bovine Solute Carrier Family 11 A1 (SLC11A1). J. Comput. Aid. Mol. Des. Feb; 33(2):265-285. doi: 10.1007/s10822-018-0179-x.
  16. Tsiolaki, P.L., Nasi, G.I., Baltoumas, F.A., Louros, N.N., Magafa, V., Hamodrakas, S.J. & Iconomidou, V.A. (2018) αCGRP, another amyloidogenic member of the CGRP family. J. Struct. Biol. Jul; 203(1):27-36. doi: 10.1016/j.jsb.2018.02.008.
  17. Louros, Ν.Ν., Tsiolaki, P.L., Baltoumas, F.A., Chryssikos, G.D., Gionis, V., Hamodrakas, S.J. & Iconomidou, V.A. (2017) Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy. J. Struct. Biol. Aug; 199 (2): 140-152. doi: 10.1016/j.jsb.2017.06.002.
  18. Baltoumas, F.A., Theodoropoulou, M.C., Hamodrakas, S.J. (2016) Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. J. Comput. Aided. Mol. Des. Jun;30(6):489-512. doi: 10.1007/s10822-016-9919-y.
  19. Louros, N.N., Baltoumas, F.A., Hamodrakas, S.J. & Iconomidou, V.A. (2016) A β-solenoid model for the Pmel17 Repeat Domain: Insights to the formation of functional amyloid fibrils. J. Comput. Aided. Mol. Des. Feb; 30 (2): 153-64. doi: 10.1007/s10822-015-9892-x.
  20. Baltoumas, F.A., Theodoropoulou, M.C. & Hamodrakas, S.J. (2013) Interactions of the α-subunits of heterotrimeric G-proteins with GPCRs, effectors and RGS proteins: a critical review and analysis of interacting surfaces, conformational shifts, structural diversity and electrostatic potentials. J. Struct. Biol. Jul; 182 (3), 209-218. doi: 10.1016/j.jsb.2013.03.004.