Peer-reviewed Publications

 
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Preprints

  1. Zhao, J., Baltoumas, F.A., Konnaris, M.A., Mouratidis, I., Liu, Z., Sims, J., Agarwal, V., Pavlopoulos, G.A., Georgakopoulos-Soares, I., Ahituv, N. (2023) MPRAbase: the massively parallel reporter assay database. bioRxiv, 2023.11.19.567742; doi: https://doi.org/10.1101/2023.11.19.567742.
  2. Mouratidis, I., Konnaris, M.A., Chantzi, N., Chan, C.S.Y., Montgomery, A., Baltoumas, F.A., Mareboina, M., Pavlopoulos, G.A.,Chartoumpekis, D.V., Georgakopoulos-Soares, I. (2023) Nucleic Quasi-Primes: Identification of the Shortest Unique Oligonucleotide Sequences in a Species. bioRxiv, 2023.12.12.571240; doi: https://doi.org/10.1101/2023.12.12.571240.

 

Published

  1. Aplakidou, E., Vergoulidis, N., Chasapi, M., Venetsianou, N.K., Kokoli, M., Panagiotopoulou, E., Iliopoulos, I., Karatzas, E., Pafilis, E., Georgakopoulos-Soares, I., Pavlopoulos, G.A., Baltoumas, F.A. (2024) Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational & Structural Biotechnology Journal, 2024 Dec:23:2011-2033; doi: https://doi.org/10.1016/j.csbj.2024.04.060
  2. Mouratidis, I., Baltoumas, F.A., Chatzi, N., Patsakis, M., Chan, C.S.Y., Montgomery, A., Konnaris, M.A., Aplakidou, E., Georgakopoulos, G.C., Das, A., Chartoumpekis, D.V., Kovac, J., Pavlopoulos, G.A., Georgakopoulos-Soares, I. (2024) kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species. Computational & Structural Biotechnology Journal, 2024 Apr 21:23:1919-1928; doi: https://doi.org/10.1016/j.csbj.2024.04.050
  3. Baltoumas, F.A., Karatzas, E., Liu, S., Ovchinnikov, S., Chen, I.M, Kyrpides, N.C., Pavlopoulos, G.A. (2024) NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Research, 2024 Jan 5;52(D1):D502-D512; doi: https://doi.org/10.1093/nar/gkad800.
  4. Tzaferis, C., Karatzas, E., Baltoumas, F.A., Pavlopoulos, G.A., Kollias, G., Konstantopoulos, D. (2023) SCALA: A web application for multimodal analysis of single cell next generation sequencing data. Computational & Structural Biotechnology Journal, 2023 Oct 20:21:5382-5393; doi: https://doi.org/10.1016/j.csbj.2023.10.032
  5. Pavlopoulos GA., Baltoumas FA., Liu S., Selvitopi O., Nayfach S., Azad A., Call L., Pedro Camargo A., Ivanova NN., Chen IM., Paez-Espino D., Karatzas E., Novel Metagenome Protein Families Consortium, Iliopoulos I., Konstantinidis K., Tiedje JM., Baker D., Ouzounis CA., Ovchinnikov S., Buluç A., Kyrpides NC. (2023) Unraveling the functional dark matter through global metagenomics. Nature 622, 594–602; doi: https://doi.org/10.1038/s41586-023-06583-7.
  6. 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. Bioinformatics, Volume 39, Issue 8, August 2023, btad490; doi: https://doi.org/10.1093/bioinformatics/btad490
  7. 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. NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad053; doi: https://doi.org/10.1093/nargab/lqad053.
  8. 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: https://doi.org/10.3389/fbinf.2023.1157956.
  9. 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: https://doi.org/10.3390/biom13020270.
  10. 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 (Basel), 2023 13 (62); doi: https://doi.org/10.3390/membranes13010062.
  11. 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: https://doi.org/10.1093/bioadv/vbac036.
  12. 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: https://doi.org/10.3390/biom12040520.
  13. 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: https://doi.org/10.1093/nargab/lqab090.
  14. 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: https://doi.org/10.3390/biom11081245.
  15. 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 2021, 10, 665. doi: https://doi.org/10.3390/biology10070665.
  16. 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. Comput Biol Med. Vol. 135, Aug. 2021, 104557. doi: https://doi.org/10.1016/j.compbiomed.2021.104557.
  17. Karatzas, E., Baltoumas, F.A., Panayiotou, N.A., Schneider, R., Pavlopoulos, G.A. (2021) Arena3Dweb: Interactive 3D visualization of multilayered networks. Nucleic Acids Research, 2021 Apr 22; gkab278. doi: https://doi.org/10.1093/nar/gkab278.
  18. 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: https://doi.org/10.1021/acs.jproteome.9b00754.
  19. 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: https://doi.org/10.1016/j.jsb.2019.06.001.
  20. 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: https://doi.org/10.1002/jcc.25823.
  21. 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: https://doi.org/10.3390/ijms20092274.
  22. 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: https://doi.org/10.1007/s10822-018-0179-x.
  23. 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: https://doi.org/10.1016/j.jsb.2018.02.008. Journal Cover Article
  24. Louros, Ν.Ν., Tsiolaki, P.L., Baltoumas, F.A., Chryssikos, G.D., Gionis, V., Hamodrakas, S.J. & Iconomidou, V.A. (2017) “Tracking down the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy”.  J. Struct. Biol. Aug; 199 (2): 140-152. doi: https://doi.org/10.1016/j.jsb.2017.06.002. Journal Cover Article
  25. 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: https://doi.org/10.1007/s10822-016-9919-y.
  26. 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: https://doi.org/10.1007/s10822-015-9892-x.
  27. 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: https://doi.org/10.1016/j.jsb.2013.03.004. Journal Cover Article