Stathatos I, Koumandou VL (2023) Comparative analysis of prokaryotic extracellular vesicle proteins and their targeting signals. Microorganisms 11(8):1977 https://doi.org/10.3390/microorganisms11081977
Valli AT, Koumandou VL, Iatrou G, Andreou M, Papasotiropoulos V, Trigas P (2021) Conservation biology of threatened Mediterranean chasmophytes: The case of Asperula naufraga endemic to Zakynthos island (Ionian islands, Greece) PLoS ONE 16(2):e0246706 https://doi.org/10.1371/journal.pone.0246706
2020
Koumandou VL, Papageorgiou L, Champeris Tsaniras S, Papathanassopoulou A, Hagidimitriou M, Cosmidis N, Vlachakis D (2019) Microbiome highjacking towards an integrative pest management pipeline. Advances in Experimental Medicine and Biology 1195:21-32. https://doi.org/10.1007/978-3-030-32633-3_4
Papageorgiou L, Loukatou S, Koumandou VL, Makalowski W, Megalooikonomou V, Vlachakis D, Kossida S (2014) Structural models for the design of novel antiviral agents against Greek Goat Encephalitis. PeerJ 2:e664 https://doi.org/10.7717/peerj.664
Koumandou VL, Kossida S (2014) Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. PLoS Computational Biology 10(9):e1003821 http://doi.org/10.1371/journal.pcbi.1003821
Karamichali I, Koumandou VL, Karagouni AD, Kossida S (2014) Frequent gene fissions associated with human pathogenic bacteria. Genomics 103(1): 65-75 http://doi.org/10.1016/j.ygeno.2014.02.001
Porcel BM, Denoeud F, Opperdoes F, Noel B, Madoui MA, Hammarton TC, Field MC, Da Silva C, Couloux A, Poulain J, Katinka M, Jabbari K, Aury JM, Campbell DA, Cintron R, Dickens NJ, Docampo R, Sturm NR, Koumandou VL, Fabre S, Flegontov P, Lukeš J, Michaeli S, Mottram JC, Szöőr B, Zilberstein D, Bringaud F, Wincker P, Dollet1 M (2014) The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PLoS Genetics 10(2):e1004007 http://doi.org/10.1371/journal.pgen.1004007
2013
Papageorgiou L, Vlachakis D, Koumandou VL, Papangelopoulos N, Kossida S (2013) Computer-aided drug design and biological evaluation of novel anti-Greek Goat Encephalitis agents. International Journal of Systems Biology and Biomedical Technologies 2(4):1-16 https://doi.org/10.4018/ijsbbt.2013100101
Koumandou VL, Wickstead B, Ginger M, van der Giezen M, Dacks JB, Field MC (2013) Molecular paleontology and complexity in the last eukaryotic common ancestor. Critical Reviews In Biochemistry & Molecular Biology 48(4):373-396 http://doi.org/10.3109/10409238.2013.821444
Trimpalis P, Koumandou VL, Pliakou E, Anagnou NP, Kossida S (2013) Gene fusion analysis in the battle against the African endemic sleeping sickness. PLoS ONE 8(7):e68854 http://doi.org/10.1371/journal.pone.0068854
Koumandou VL, Scorilas A (2013) Evolution of the plasma and tissue kallikreins and their alternative splicing isoforms. PLoS ONE 8(7):e68074 http://doi.org/10.1371/journal.pone.0068074
Vlachakis D, Koumandou VL, Kossida S (2013) A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase. PeerJ 1:e74 https://doi.org/10.7717/peerj.74
Koumandou VL, Boehm C, Horder K, Field MC (2013) Evidence for recycling of invariant surface transmembrane domain proteins in African trypanosomes. Eukaryotic Cell 12:330-342 https://doi.org/10.1128/EC.00273-12
2012
Tsagrasoulis D, Danos V, Kissa M, Trimpalis P, Koumandou VL, Karagouni AD, Tsakalidis A, Kossida S (2012) SAFE software and FED database to uncover protein-protein interactions using gene fusion. Evolutionary Bioinformatics 8:47-60 http://doi.org/10.4137/EBO.S8018
2011
Dimitriadis D, Koumandou VL, Trimpalis P, Kossida S (2011) Protein functional links in Trypanosoma brucei, identified by gene fusion analysis. BMC Evolutionary Biology 11:193 https://doi.org/10.1186/1471-2148-11-193
Koumandou VL, Herman E, Klute M, Nunez-Miguel R, Dacks JB, Field MC (2011) Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei. Journal of Cell Science 124:1496-1509 https://doi.org/10.1242/jcs.081596
2008
Koumandou VL, Natesan SKA, Sergeenko T, Field MC (2008) The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages. BMC Genomics 9:298 https://doi.org/10.1186/1471-2164-9-298
2007
Berdalet E, Peters F, Koumandou VL, Roldán C, Guadayol O, Estrada M (2007) Species-specific physiological response of dinoflagellates to small-scale turbulence. Journal of Phycology 43:965-977 http://doi.org/10.1111/j.1529-8817.2007.00392.x
Koumandou VL, Dacks JB, Coulson RMR, Field MC (2007) Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins. BMC Evolutionary Biology 7:29 https://doi.org/10.1186/1471-2148-7-29
Koumandou VL, Howe CJ (2007) The copy number of chloroplast gene minicircles changes dramatically with growth phase in the dinoflagellate Amphidinium operculatum. Protist 158(1):89-103 https://doi.org/10.1016/j.protis.2006.08.003
Koumandou VL, Nisbet RE, Barbrook AC, Howe CJ (2004) Dinoflagellate chloroplasts: where have all the genes gone? Review. Trends in Genetics 20:261-267 https://doi.org/10.1016/j.tig.2004.03.008
Nisbet RE, Koumandou LV, Barbrook AC, Howe CJ (2004) Novel plastid gene minicircles in the dinoflagellate A. operculatum. Gene 331:141-147 https://doi.org/10.1016/j.gene.2004.02.008
2003
Howe CJ, Barbrook AC, Koumandou VL, Nisbet RE, Symington HA, Wightman TF (2003) Evolution of the chloroplast genome. Philosophical Transactions of the Royal Society of London, Series B. 358:99-107 https://doi.org/10.1098/rstb.2002.1176
Book Chapters:
Koumandou VL, Field MC (2011) The emergence of cellular complexity at the dawn of the eukaryotes: reconstructing the endomembrane system with in silico and functional analyses. In "Evolutionary Biology - Concepts, Biodiversity, Macroevolution and Genome Evolution" pg. 153-167. http://www.springer.com/gp/book/9783642207624 Published by Springer-Verlag. Editor: Pierre Pontarotti
Koumandou VL (2008) Sequence similarity search. Book chapter in Greek in "Bioinformatics: possibilities and perspectives" pg. 71-85. https://service.eudoxus.gr/search/#a/id:5110/0 Published by the Biomedical Research Foundation of the Academy of Athens. Editor: Sophia Kossida