Publications

Visit ORCID for an updated list of publications.

2020

Mavropoulos Papoudas S, Papanikolaou N and Nikolaou C., (2020) Monitoring the prolonged TNF stimulation in space and time with topological-functional networks. Computational and Structural Biotechnology Journal, 18, 220-229. https://doi.org/10.1016/j.csbj

Papadaki C, Monastirioti A, Rounis K, Makrakis D, Kalbakis K, Nikolaou C, Mavroudis D and Agelaki S, (2020) Circulating MicroRNAs Regulating DNA Damage Response and Responsiveness to Cisplatin in the Prognosis of Patients with Non-Small Cell Lung Cancer Treated with First-Line Platinum Chemotherapy. Cancers 2020, 12(5), 1282. https://doi.org/10.3390/cancers12051282

Ntasis VF, Panousis NI, Tektonidou MG, Dermitzakis ET, Boumpas DT, Bertsias GK, Nikolaou C (2020) Extensive fragmentation and re-organization of gene co-expression patterns underlie the progression of Systemic Lupus Erythematosus https://doi.org/10.1101/2020.01.28.922559

2019

Karagianni N, Kranidioti K, Fikas N, Tsochatzidou M, Chouvardas P, Denis MC, Kollias G and Nikolaou C (2019) An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis. PLoS Computational Biology 15(5): e1006933. https://doi.org/10.1371/journal.pcbi.1006933

Salataj E, Stathopoulou C, Hafþórsson RA, Nikolaou C and Spilianakis GC (2019) Developmental Conservation of microRNA Gene Localization at the Nuclear Periphery. PLoS One, 14(11):e0223759. https://doi.org/10.1371/journal.pone.0223759.

Sachini N, Arampatzi P, Klonizakis A, Nikolaou C, Makatounakis T, Lam E W-F., Kretsovali A and Papamatheakis J (2019) Promyelocytic leukemia protein (PML) controls breast cancer cell proliferation by modulating Forkhead transcription factors. Molecular Oncology, 13, 1369-1387. https://doi.org/10.1002/1878-0261.12486

Balabanidou V, Kefi M, Aivaliotis M, Koidou V, Girotti JR, Mijailovsky SJ, Juárez MP, Papadogiorgaki E, Chalepakis G, Kampouraki A, Nikolaou C, Ranson H and Vontas J (2019) Mosquitoes cloak their legs to resist insecticides. Proceedings of the Royal Society B 20191091. https://doi.org/10.1098/rspb.2019.1091

2018

Nikolaou C (2018) Invisible Cities: Segregated Domains in the yeast genome with distinct structural and functional attributes. Current Genetics, 64 (1), 247-258. https://dx.doi.org/10.1007/s00294-017-0731-6

Joshi RS, Nikolaou C and Roca J (2018) Structural and Chromosomal Organization of Yeast Genes Regulated by Topoisomerase II. International Journal of Molecular Sciences. 19 (1), 134 https://dx.doi.org/10.3390/ijms19010134

Papadaki C, Stratigos M, Markakis G, Spiliotaki M, Mastrostamatis G, Nikolaou C, Mavroudis D and Agelaki S (2018) Circulating microRNAs in the early prediction of disease recurrence in primary breast cancer. Breast Cancer Research. 201820:72 https://doi.org/10.1186/s13058-018-1001-3

Chanoumidou K, Hadjimichael C, Athanasouli P, Ahlenius H, Klonizakis A, Nikolaou C, Drakos E, Kostouros A, Stratidaki I, Grigoriou M, Kretsovali A. (2018) Groucho related gene 5 (GRG5) is involved in embryonic and neural stem cell state decisions. Sci Rep. 2018 Sep 13;8(1):13790. https://doi.org/10.1038/s41598-018-31696-9

ECCB 2018 Steering Committee, Hatzigeorgiou AG, Bagos P, Benos PV, Nikolaou C, Moreau Y and Kavakiotis I. (2018) ECCB 2018: The 17th European Conference on Computational Biology. Bioinformatics, 34, (17), i595–i598. https://doi.org/10.1093/bioinformatics/bty740

2017

Hadjimichael C, Chanoumidou K, Nikolaou C, Klonizakis A, Theodosi GI, Makatounakis T, Papamatheakis J and Kretsovali A. (2017) Promyelocytic Leukemia (PML) protein is an essential regulator of stem cell pluripotency and somatic cell reprogramming. Stem Cell Reports, 8 (5), 1366-1378 http://dx.doi.org/10.1016/j.stemcr.2017.03.006

Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J and Nikolaou C. (2017). Genome urbanization: Clusters of topologically co-regulated genes delineate functional compartments in the genome of S. cerevisiae. Nucleic Acids Research, 45 (10), 5818-5828. https://dx.doi.org/10.1093/nar/gkx198

Ntougkos E, Chouvardas P, Roumelioti F, Ospelt C, Frank-Bertoncelj M, Fihler A, Buckley CD, Gay S, Nikolaou C# and Kollias G# (2017) Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis. Arthritis and Rheumatology, 69 (8): 1588-1600. https://dx.doi.org/10.1002/art.40128

2016

Hadjimichael C, Nikolaou C, Papamatheakis J and Kretsovali A. (2016) MicroRNAs for Fine-Tuning of Mouse Embryonic Stem Cell Fate Decision through Regulation of TGF-β Signaling. Stem Cell Reports 6 (3): 292-301 http://dx.doi.org/10.1016/j.stemcr.2016.01.004

Chouvardas P, Kollias G and Nikolaou C. (2016) Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. BMC Bioinformatics 17(5):181 http://dx.doi.org/10.1186/s12859-016-1040-7

Michopoulos F, Karagianni N, Whalley NM, Firth MA, Nikolaou C, Wilson ID, Critchlow SE, Kollias G, Theodoridis GA (2016) Targeted Metabolic Profiling of the Tg197 Mouse Model Reveals Itaconic Acid as a Marker of Rheumatoid Arthritis. Journal of Proteome Research 15 (12): 4579-4590 http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00654

2015

Apostolou-Karampelis K, Nikolaou C and Almirantis Y. (2016) A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms. DNA Research 23 (4): 353-363 https://doi.org/10.1093/dnares/dsw021

2014

Roulis M, Nikolaou C, Kotsaki E, Kaffe E, Karagianni N, Koliaraki V, Salpea K, Ragoussis J, Aidinis V, Martini E, Becker C, Herschman HR, Vetrano S, Danese S and Kollias G (2014) Intestinal myofibroblast-specific Tpl2-Cox-2-PGE2 pathway links innate sensing to epithelial homeostasis. Proceedings of the National Academy of Sciences, U.S.A. 111 (43): E4658-E4667 http://dx.doi.org/10.1073/pnas.1415762111

Andreadis C, Nikolaou C, Fragiadakis GS, Tsiliki G and Alexandraki D (2014) Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae. Nucleic Acids Research42 (20): 12650-12667 https://doi.org/10.1093/nar/gku915

Nikolaou C. (2014) Menzerath–Altmann law in mammalian exons reflects the dynamics of gene structure evolution. Computational Biology and Chemistry, 53: 134-143 http://dx.doi.org/10.1016/j.compbiolchem.2014.08.018

Tsiagkas K, Nikolaou C and Almirantis Y. (2014) Orphan and gene related CpG Islands follow power-law-like distributions in several genomes: Evidence of function-related and taxonomy-related modes of distribution. Computational Biology and Chemistry, 53: 84-96 http://dx.doi.org/10.1016/j.compbiolchem.2014.08.013

2009-2013 (on Nucleosome Positioning)

Tilgner H#, Nikolaou C#, Althammer S, Sammeth M, Beato M, Valcárcel J and Guigo R. (2009) Nucleosome positioning as a determinant of exon recognition. Nature Structural & Molecular Biology, 16(9):996-1001. http://dx.doi.org/10.1038/nsmb.1658

Nikolaou C, Althammer S, Beato M and Guigo R. (2010) Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics and Chromatin 3 (1) 20 http://dx.doi.org/10.1186/1756-8935-3-20

Nikolaou C, Bermudez I, Manichanh C, García-Martinez J, Guigo R, Perez-Ortin JE and Roca J (2013) Topoisomerase II regulates yeast genes with singular chromatin architectures. Nucleic Acids Research 41 (20): 9243-9256 http://dx.doi.org/10.1093/nar/gkt707

2006-2008 (on Genome Architecture in Prokaryotes)

Nikolaou C and Almirantis Y (2005) A Study on the correlation of nucleotide skews and the positioning of the Origin of Replication. Different modes of replication in bacterial species. Nucleic Acids Research, 33, 6816-6822 https://doi.org/10.1093/nar/gki988

Nikolaou C and Almirantis Y (2006) Deviations from Chargaff's second parity rule in organellar DNA Insights into the evolution of organellar genomes. Gene , 381:34-41 http://dx.doi.org/10.1016/j.gene.2006.06.010

2002-2005 (on Sequence Analysis and Gene Finding)

Nikolaou C and Almirantis Y (2002) A study of the middle-scale nucleotide clustering in DNA sequences of various origin and functionality, by means of a method based on a Modified Standard Deviation. Journal of Theoretical Biology, 217, 479-492 http://dx.doi.org/10.1006/jtbi.2002.3045

Nikolaou C and Almirantis Y (2003) Mutually symmetric and complementary triplets: Differences in their use distinguish systematically between coding and non-coding genomic sequences. Journal of Theoretical Biology, 223, 477-487 http://dx.doi.org/10.1016/S0022-5193(03)00123-1

Nikolaou C and Almirantis Y (2004) Measuring the Coding Potential of Genomic Sequences through a combination of Triplet Occurrence Patterns and RNY Preference. Journal of Molecular Evolution, 59, 309-316 http://dx.doi.org/10.1007/s00239-004-2626-7

Almirantis Y and Nikolaou C (2005) Multi-criterial Coding Sequence Prediction. Combination of GeneMark with two novel, coding character-specific quantities. Computers in Biology and Medicine, 35, 627-643 http://dx.doi.org/10.1016/j.compbiomed.2004.04.002

Nikolaou C and Almirantis Y (2005) 'Word' preference in the genomic text and genome evolution. Different modes of n-tuplet usage in coding and noncoding sequences. Journal of Molecular Evolution, 61, 23-35 http://dx.doi.org/10.1007/s00239-004-0209-2

 

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