Published

ASTRA: A comprehensive resource of stress-induced transcriptional activity in human cell lines
Tsifintaris M, Grigoriadis D, Sitmalidis M, Repanas P, Lazarashvili KE, Anastasiadi C, Kavakiotis I, Sandaltzopoulos R, Pavlopoulos GA, Giannakakis A.
Nucleic Acids Res. 2025. (In press). [ARTICLE]

metagRoot: A comprehensive database of protein families associated with plant root microbiomes
Chasapi MN, Chasapi IN, Aplakidou E, Baltoumas FA, Karatzas E, Iliopoulos I, Stravopodis DJ, Emiris IZ, Buluç A, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA.
Nucleic Acids Res. 2025 Sep 1. doi:10.1093/nar/gkaf862. PMID:40888850. [ARTICLE]

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life
Chantzi N, Nayak A, Baltoumas FA, Aplakidou E, Liew SW, Galuh JE, Patsakis M, Moeckel C, Mouratidis I, Sazed SAS, Guiblet W, Montgomery A, Karmiris-Obratanski P, Wang G, Zaravinos A, Vasquez KM, Pavlopoulos GA, Georgakopoulos-Soares I.
Genome Res. 2025 Aug 26:gr.279790.124. doi:10.1101/gr.279790.124. PMID:40858360. [ARTICLE]

Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations
Baltoumas FA, Karatzas E, Venetsianou NK, Aplakidou E, Giatras K, Chasapi MN, Chasapi IN, Iliopoulos I, Iconomidou VA, Trougakos IP, Psomopoulos F, Giannakakis A, Georgakopoulos-Soares I, Kontou P, Bagos PG, Pavlopoulos GA.
Comput Struct Biotechnol J. 2025 Jun 14;27:2626-2637. doi:10.1016/j.csbj.2025.06.025. PMID:40599243. [ARTICLE]

invertiaDB: A database of inverted repeats across organismal genomes
Provatas K, Chantzi N, Amptazi N, Patsakis M, Nayak A, Mouratidis I, Zaravinos A, Pavlopoulos GA, Georgakopoulos-Soares I.
Nucleic Acids Res. 2025 Apr 22;53(8):gkaf329. doi:10.1093/nar/gkaf329. PMID:40272360. [ARTICLE]

MPRAbase: A massively parallel reporter assay database
Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N.
Genome Res. 2025 Apr 22:gr.280387.124. doi:10.1101/gr.280387.124. PMID:40262894. [ARTICLE]

Multimodal SARS-CoV-2 interactome sketches the virus–host spatial organization
Dugied G, Laurent EMN, Attia M, Gimeno JP, Bachiri K, Samavarchi-Tehrani P, Donati F, Rahou Y, Munier S, Amara F, Dos Santos M, Soler N, Volant S, Pietrosemoli N, Gingras AC, Pavlopoulos GA, van der Werf S, Falter-Braun P, Jacob Y, Komarova A, Sofianatos Y, Demeret C, Coyaud E.
Commun Biol. 2025 Mar 26;8(1):501. doi:10.1038/s42003-025-07933-z. PMID:40140549. [ARTICLE]

MAFin: Motif detection in multiple alignment files
Patsakis M, Provatas K, Baltoumas FA, Chantzi N, Mouratidis I, Pavlopoulos GA, Georgakopoulos-Soares I.
Bioinformatics. 2025 Mar 19:btaf125. doi:10.1093/bioinformatics/btaf125. PMID:40106711. [ARTICLE]

APNet, an explainable sparse deep learning model to discover differentially active drivers of severity from COVID-19 multi-omics
Gavriilidis GI, Vasileiou V, Dimitsaki S, Karakatsoulis G, Giannakakis A, Pavlopoulos GA, Psomopoulos F.
Bioinformatics. 2025 Feb 8:btaf063. doi:10.1093/bioinformatics/btaf063. PMID:39921901. [ARTICLE]

Identification of the shortest unique oligonucleotide sequences in a species
Mouratidis I, Konnaris MA, Chantzi N, Chan CSY, Montgomery A, Baltoumas FA, Patsakis M, Mareboina M, Pavlopoulos GA, Chartoumpekis VD, Georgakopoulos-Soares I.
Genome Res. 2025 Feb 14;35(2):279-295. doi:10.1101/gr.280070.124. PMID:39746719. [ARTICLE]

VISTA Enhancer Browser: An updated database of tissue-specific developmental enhancers
Kosicki M, Baltoumas FA, Kelman G, Boverhof J, Ong Y, Cook L, Dickel E, Diane E, Pavlopoulos GA, Pennacchio L, Visel A.
Nucleic Acids Res. 2025 Jan 6:gkae940. doi:10.1093/nar/gkae940. PMID:39470740. [ARTICLE]

BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery
Theodosiou T, Vrettos K, Baltsavia I, Baltoumas F, Papanikolaou N, Antonakis NA, Mossialos D, Ouzounis CA, Promponas VJ, Karaglani M, Chatzaki E, Brandaug S, Pavlopoulos GA, Andreakos E, Iliopoulos I.
Comput Struct Biotechnol J. 2024 Aug 21;23:3247-3253. doi:10.1016/j.csbj.2024.08.016. Epub 2024 Dec. PMID:39279874. [ARTICLE]

A survey of k-mer methods and applications in bioinformatics
Moeckel C, Mareboina M, Konnaris MA, Chan CSY, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I.
Comput Struct Biotechnol J. 2024 May 21;23:2289-2303. doi:10.1016/j.csbj.2024.05.025. Epub 2024 Dec. PMID:38840832. [ARTICLE]

Visualizing metagenomic data: A comprehensive review
Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA.
Comput Struct Biotechnol J. 2024 May 3;23:2011-2033. doi:10.1016/j.csbj.2024.04.060. PMID:38765606. [ARTICLE]

kmerDB: A database encompassing the set of genomic and proteomic sequence information of each species
Mouratidis I, Baltoumas FA, Chantzi N, Patsakis M, Chan SY, Montgomery A, Konnaris MA, Aplakidou E, Georgakopoulos GC, Das A, Chartoumpekis D, Kovac J, Pavlopoulos GA, Georgakopoulos-Soares I.
Comput Struct Biotechnol J. 2024 Apr 21;23:1919-1928. doi:10.1016/j.csbj.2024.04.050. PMID:38711760. [ARTICLE]

SCALA: A complete solution for multimodal analysis of single-cell next generation sequencing data
Tzaferis C, Karatzas E, Baltoumas FA, Pavlopoulos GA, Kollias GK, Konstantopoulos D.
Comput Struct Biotechnol J. 2023 Oct 20. doi:10.1016/j.csbj.2023.10.032. PMID:38022693. [ARTICLE]

Unraveling the functional dark matter through global metagenomics
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Nayfach S, Azad A, Call L, Camargo AP, 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.
Nature. 2023 Oct;622(7983):594-602. Epub 2023 Oct 11. doi:10.1038/s41586-023-06583-7. PMID:37821698. [ARTICLE]

NMPFamsDB: A database of novel protein families from microbial metagenomes and metatranscriptomes
Baltoumas FA, Karatzas E, Liu S, Ovchinnikov S, Sofianatos Y, Chen IM, Kyrpides NC, Pavlopoulos GA.
Nucleic Acids Res. 2023 Oct 9:gkad800. doi:10.1093/nar/gkad800. PMID:37811892. [ARTICLE]

FLAME (v2.0): Advanced integration and interpretation of functional enrichment results from multiple sources
Karatzas E, Baltoumas FA, Aplakidou E, Kontou PI, Stathopoulos P, Stefanis L, Bagos PG, Pavlopoulos GA.
Bioinformatics. 2023 Aug 1;39(8):btad490. doi:10.1093/bioinformatics/btad490. PMID:37540207. [ARTICLE]

Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration
Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva TN, Jensen LJ, Pavlopoulos GA.
NAR Genom Bioinform. 2023 Jun;5(2):lqad053. doi:10.1093/nargab/lqad053. PMID:37260509. [ARTICLE]

Exploring microbial functional biodiversity at the protein family level: From metagenomic sequence reads to annotated protein clusters
Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou N, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA.
Front Bioinform. 2023 Mar 3;3:1157956. doi:10.3389/fbinf.2023.1157956. PMID:36959975. [ARTICLE]

Ageotypes revisited: The brain and central nervous system dysfunction as a major nutritional and lifestyle target for healthy aging
Skoufas E, Kanellakis S, Sanoudou D, Eliopoulos AG, Pavlopoulos GA, Gkouskou KK.
Maturitas. 2023 Feb 6. doi:10.1016/j.maturitas.2023.01.013. PMID:36773500. [ARTICLE]

Drug genetic associations with COVID-19 manifestations: A data mining and network biology approach
Charitou T, Kontou PI, Tamposis IA, Pavlopoulos GA, Braliou GG, Bagos PG.
Pharmacogenomics J. 2022 Sep 28. doi:10.1038/s41397-022-00289-1. PMID:36171417. [ARTICLE]

IL-6 signaling attenuates TNF-α production by plasmacytoid DCs in rheumatoid arthritis
Papadaki G, Goutakoli P, Tiniakou I, Grün JR, Grützkau A, Pavlopoulos GA, Iliopoulos I, Bertsias G, Boumpas D, Ospelt C, Reizis B, Sidiropoulos P, Verginis P.
J Immunol. 2022 Sep 23:ji2100882. doi:10.4049/jimmunol.2100882. Epub ahead of print. PMID:36426957. [ARTICLE]

Prediction and validation of biomarkers using multiple UniReD
Baltsavia I, Theodosiou T, Papanikolaou N, Pavlopoulos GA, Amoutzias GD, Panagopoulou M, Chatzaki E, Andreakos E, Iliopoulos I.
Int J Mol Sci. 2022;23(19):11112. doi:10.3390/ijms231911112. PMID:36232413. [ARTICLE]

Consolidated variant calling from whole exome sequencing data using three variant callers
Verrou KM, Pavlopoulos GA, Moulos P.
STAR Protoc. 2022 Jun 4;3(2):101418. doi:10.1016/j.xpro.2022.101418. PMID:35669050. [ARTICLE]

The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E, Koutrouli M, Baltoumas F, Papanikolopoulou K, Bouyioukos C, Pavlopoulos GA.
Bioinform Adv. 2022 May 13:vbac036. doi:10.1093/bioadv/vbac036. PMID:36699373. [ARTICLE]

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey
Galanis A, Vardakas P, Reczko M, Harokopos V, Hatzis P, Skoulakis E, Pavlopoulos GA, Patalano S.
Mol Ecol Resour. 2022 May 20. doi:10.1111/1755-0998.13626. PMID:35593171. [ARTICLE]

DARLING: A web application for detecting disease-related biomedical entity associations using literature mining
Karatzas E, Baltoumas FA, Kasionis I, Sanoudou D, Eliopoulos GA, Theodosiou T, Iliopoulos I, Pavlopoulos GA.
Biomolecules. 2022 Mar 30;12(4):520. doi:10.3390/biom12040520. PMID:35454109. [ARTICLE]

PREGO: A literature and data-mining resource to associate microorganisms, biological processes and environment types
Zafeiropoulos H, Paragkamian S, Ninidakis S, Pavlopoulos GA, Jensen LJ, Pafilis E.
Microorganisms. 2022;10:293. doi:10.3390/microorganisms10020293. PMID:35208748. [ARTICLE]

Extreme-scale many-against-many protein similarity search
Selvitopi O., Ekanayake S., Guidi G., Awan M., Pavlopoulos GA., Azad A., Kyrpides N., Oliker L., Yelick K., Buluç A..
IEEE/ACM SC22: International Conference for High Performance Computing, Networking, Storage and Analysis, Dallas, TX, US, 2022, pp. 1-12. ACM Gordon Bell Prize award finalist [Link] [ACM Gordon Bell Prize award finalist] [CONFERENCE]

OnTheFly2.0: A text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos GA, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA.
NAR Genom Bioinform. 2021 Dec;3(4):lqab090. doi:10.1093/nargab/lqab090. PMID:34632381. [ARTICLE]

Blood transcriptomes of anti-SARS-CoV-2 antibody-positive asymptomatic versus symptomatic individuals
Sfikakis PP, Verrou KM, Ampatziadis-Michailidis G, Tsitsilonis O, Paraskevis D, Kastritis E, Lianidou E, Moutsatsou P, Terpos E, Trougakos I, Chini V, Manoloukos M, Moulos P, Pavlopoulos GA, Kollias G, Hatzis P, Dimopoulos MA.
Front Immunol. 2021 Oct 5;12:746203. doi:10.3389/fimmu.2021.746203. PMID:34675930. [ARTICLE]

Biomolecule and bioentity interaction databases in systems biology: A comprehensive review
Baltoumas FA, Zafeiropoulou S, Karatzas E, Koutrouli M, Thanati F, Voutsadaki K, Gkonta M, Hotova J, Kasionis I, Hatzis P, Pavlopoulos GA.
Biomolecules. 2021;11:1245. doi:10.3390/biom11081245. PMID:34439912. [ARTICLE]

FLAME: A web tool for functional and literature enrichment analysis using multiple gene lists
Thanati F, Karatzas E, Baltoumas F, Stravopodis DJ, Eliopoulos AG, Pavlopoulos GA.
Biology (Basel). 2021 Jul 14;10(7):665. doi:10.3390/biology10070665. PMID:34356520. [ARTICLE]

Molecular epidemiology of SARS-CoV-2 in Greece demonstrates low rates of onward virus transmission despite the lift in summer travel restrictions
Kostaki EG, Pavlopoulos GA, Verrou KM, Michailidis GA, Harokopos V, Hatzis P, Moulos P, Siafakas N, Pournaras S, Hadjichristodoulou C, et al..
mSphere. 2021 Jun 30;6(4):e00180-21. doi:10.1128/mSphere.00180-21. PMID:34190583. [ARTICLE]

NORMA—the network makeup artist: A web tool for network annotation visualization
Koutrouli M, Karatzas E, Papanikolopoulou K, Pavlopoulos GA.
Genomics Proteom Bioinform. 2021 Jun 22:S1672-0229(21)00130-3. doi:10.1016/j.gpb.2021.02.005. PMID:34171457. [ARTICLE]

VICTOR: A visual analytics web application for comparing cluster sets
Karatzas E, Gkonta M, Hotova J, Baltoumas FA, Kontou PI, Bobotsis CJ, Bagos PG, Pavlopoulos GA.
Comput Biol Med. 2021 Jun 8;135:104557. doi:10.1016/j.compbiomed.2021.104557. PMID:34139436. [ARTICLE]

The network analysis profiler (NAP v2.0): A web tool for easier topological analysis and comparison of medium-scale biological networks
Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA.
EMBnet.journal. 2021;26:e943. [ARTICLE]

ProteoSign v2: A faster and evolved user-friendly online tool for statistical analyses of differential proteomics
Theodorakis V, Antonakis AN, Baltsavia I, Pavlopoulos GA, Samiotaki M, Amoutzias G, Theodosiou T, Acuto O, Efstathiou G, Iliopoulos I.
Nucleic Acids Res. 2021 May 8:gkab329. doi:10.1093/nar/gkab329. PMID:33963869. [ARTICLE]

Arena3Dweb: Interactive 3D visualization of multilayered networks
Karatzas E, Baltoumas FA, Panayiotou NA, Schneider R, Pavlopoulos GA.
Nucleic Acids Res. 2021 Apr 22:gkab278. doi:10.1093/nar/gkab278. PMID:33885790. [ARTICLE]

Distinct transcriptional profile of blood mononuclear cells in Behçet’s disease: Insights into the central role of neutrophil chemotaxis
Verrou KM, Vlachogiannis NI, Ampatziadis-Michailidis G, Moulos P, Pavlopoulos GA, Hatzis P, Kollias G, Sfikakis PP.
Rheumatology (Oxford). 2021 Jan 25;keab052. doi:10.1093/rheumatology/keab052. PMID:33493315. [ARTICLE]

The human GPCR signal transduction network
Kontou P, Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos GA, Hamodrakas S, Bagos PG.
Netw Model Anal Health Inform Bioinform. 2021;10:3. doi:10.1007/s13721-020-00278-z. [ARTICLE]

Exploring networks in the STRING & REACTOME database
Koutrouli M, Hatzis P, Pavlopoulos GA.
Systems Medicine: Integrative, Qualitative and Computational Approaches. Wolkenhauer O (ed.). 2021; vol. 3:507–520. Oxford: Elsevier. ISBN: 9780128012383. DOI: 10.1016/B978-0-12-801238-3.11516-8 [DOI] [BOOK CHAPTER]

Structure determination of the HgcAB complex using metagenome sequence data: Insights into microbial mercury methylation
Cooper CJ, Zheng K, Rush WK, Johs A, Sanders BC, Pavlopoulos GA, Kyrpides NC, Podar M, Ovchinnikov S, Ragsdale SW, Parks JM.
Commun Biol. 2020 Jun 19;3(1):320. doi:10.1038/s42003-020-1047-5. PMID:32561885. [ARTICLE]

UniProt Related Documents (UniReD): Assisting wet-lab biologists in their quest on finding novel counterparts in a protein network
Theodosiou T, Papanikolaou N, Savvaki M, Bonetto G, Maxouri S, Fakoureli E, Eliopoulos GA, Tavernarakis N, Amoutzias GD, Pavlopoulos GA, Aivaliotis M, Nikoletopoulou V, Tzamarias D, Iliopoulos I.
NAR Genom Bioinform. 2020 Mar;2(1):lqaa005. doi:10.1093/nargab/lqaa005. PMID:33575553. [ARTICLE]

A guide to conquer the biological network era using graph theory
Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA.
Front Bioeng Biotechnol. 2020 Jan 31;8:34. doi:10.3389/fbioe.2020.00034. PMID:32083072. [ARTICLE]

PASTIS: Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Selvitopi O, Ekanayake S, Guidi G, Pavlopoulos GA, Azad A, Buluc A..
SC20: International Conference for High Performance Computing, Networking, Storage and Analysis, November 2020. [Link] [YouTube] [CONFERENCE]

Diversity, evolution, and classification of virophages uncovered through global metagenomics
Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC.
Microbiome. 2019 Dec 10;7(1):157. doi:10.1186/s40168-019-0768-5. PMID:31823797. [ARTICLE]

Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions
Sberro H, Fremin JB, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS.
Cell. 2019 Aug 8;178(4):1245-1259.e14. doi:10.1016/j.cell.2019.07.016. PMID:31402174. [ARTICLE]

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D, et al..
Nat Biotechnol. 2018 Mar 19;36(4):359-367. doi:10.1038/nbt.4110. PMID:29553575. [ARTICLE]

Bipartite graphs in systems biology and medicine: A survey of methods and applications
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bougioukos C, Markou E, Bagos PG.
GigaScience. 2018 Apr 1;7(4):giy014. doi:10.1093/gigascience/giy014. PMID:29648623. [ARTICLE]

HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks
Azad A, Pavlopoulos GA, Ouzounis C, Kyrpides NC, Buluç A.
Nucleic Acids Res. 2018 Jan 5;46(6):e33. doi:10.1093/nar/gkx1313. PMID:29315405. [ARTICLE]

Empirical comparison of visualization tools for larger-scale network analysis
Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I.
Adv Bioinformatics. 2017;2017:1278932. doi:10.1155/2017/1278932. PMID:28804499. [ARTICLE]

Non-targeted virus sequence discovery pipeline and virus clustering for metagenomic data
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC.
Nat Protoc. 2017 Aug;12(8):1673-1682. doi:10.1038/nprot.2017.063. PMID:28749930. [ARTICLE]

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks
Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA.
BMC Res Notes. 2017;10:278. doi:10.1186/s13104-017-2607-8. PMID:28705239. [ARTICLE]

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, et al..
Nat Biotechnol. 2017 Jun 12;35(7):676-683. doi:10.1038/nbt.3886. PMID:28604660. [ARTICLE]

ProteoSign: An end-user online differential proteomics statistical analysis platform
Efstathiou G, Antonakis AN, Pavlopoulos GA, Theodosiou T, Divanach P, Trudgian DC, Thomas B, Papanikolaou N, Aivaliotis M, Acuto O, Iliopoulos I.
Nucleic Acids Res. 2017 May 17;45(W1):W128-W133. doi:10.1093/nar/gkx444. PMID:28520987. [ARTICLE]

Protein structure determination using metagenome sequence data
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D.
Science. 2017 Jan 20;355(6322):294-298. doi:10.1126/science.aah4043. PMID:28104891. [ARTICLE]

IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses
Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, Reddy TBK, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu W, Rivers AR, Ivanova NN, Kyrpides NC.
Nucleic Acids Res. 2017 Oct;45(D1):D457-D465. doi:10.1093/nar/gkw1030. PMID:27799466. [ARTICLE]

Uncovering Earth’s virome
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC.
Nature. 2016 Aug 17;536(7617):425-430. doi:10.1038/nature19094. PMID:27533034. [ARTICLE]

DrugQuest: A text-mining workflow for drug association discovery
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I.
BMC Bioinformatics. 2016 Jun;17(Suppl 5):182. doi:10.1186/s12859-016-1041-6. PMID:27295093. [ARTICLE]

Data and programs in support of network analysis of genes and their association with diseases
Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG.
Data Brief. 2016 Jul 19;8:1036-1039. doi:10.1016/j.dib.2016.07.022. PMID:27508260. [ARTICLE]

Network analysis of genes and their association with diseases
Kontou PI, Pavlopoulou A, Dimou NL, Pavlopoulos GA, Bagos PG.
Gene. 2016 Sep 15;590(1):68-78. doi:10.1016/j.gene.2016.05.044. PMID:27265032. [ARTICLE]

Apolipoprotein A-I inhibits experimental colitis and colitis-propelled carcinogenesis
Gkouskou KK, Ioannou M, Pavlopoulos GA, Georgila K, Siganou A, Nikolaidis G, Kanellis DC, Moore S, Papadakis KA, Kardassis D, Iliopoulos I, McDyer FA, Drakos E, Eliopoulos AG.
Oncogene. 2015 Aug 17;34(35):4365-4379. doi:10.1038/onc.2015.307. PMID:26279300. [ARTICLE]

Visualizing genome and systems biology: Technologies, tools, implementation techniques and trends, past, present and future
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.
GigaScience. 2015 Aug 25;4:38. doi:10.1186/s13742-015-0077-2. PMID:26309733. [ARTICLE]

Metagenomics: Tools and insights for analyzing NGS sequencing data derived from biodiversity studies
Oulas A, Pavloudi C, Polymenakou P, Papanikolaou N, Pavlopoulos GA, Kotoulas G, Arvanitidis C, Iliopoulos I.
Bioinform Biol Insights. 2015 May 25;9:75-88. doi:10.4137/BBI.S12462. PMID:25983555. [ARTICLE]

Prediction of miRNA Targets
Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Iliopoulos I, Poirazi P, Kalantidis K.
RNA Bioinformatics: Methods in Molecular Biology. Humana Press, USA. 2015;1269:207–229. DOI: 10.1007/978-1-4939-2291-8_13 PMID: 25577381 [PubMed] [DOI] [BOOK CHAPTER]

Protein-protein interaction predictions using text-mining tools
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I.
Methods. 2014 Oct 28;74:47-53. doi:10.1016/j.ymeth.2014.10.026. PMID:25448298. [ARTICLE]

BioTextQuest+: A knowledge integration platform for literature mining and concept discovery
Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam V, Ouzounis C, Eliopoulos A, Promponas VJ, Iliopoulos I.
Bioinformatics. 2014;30(17):2521-2523. doi:10.1093/bioinformatics/btu524. PMID:25100685. [ARTICLE]

Biological information extraction and co-occurrence analysis
Pavlopoulos GA, Promponas V, Ouzounis C, Iliopoulos I.
Biomedical Literature Mining: Methods in Molecular Biology. Humana Press, USA. 2014;1159:77–92. ISBN-13: 978-1493907083. DOI: 10.1007/978-1-4939-0709-0_5 PMID: 24788262 [PubMed] [DOI] [BOOK CHAPTER]

Unraveling genomic variation from next-generation sequencing data
Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I.
BioData Min. 2013 Jul 6;6:13. doi:10.1186/1756-0381-6-13. PMID:23885890. [ARTICLE]

Meander: Visually exploring the structural variome using space-filling curves
Pavlopoulos GA, Sifrim A, Sakai R, Kumar P, Voet T, Moreau Y, Aerts J.
Nucleic Acids Res. 2013;41(9):e103. doi:10.1093/nar/gkt254. PMID:23605045. [ARTICLE]

OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction
Pafilis E, Pavlopoulos GA, Satagopam V, Papanikolaou N, Horn H, Arvanitidis C, Jensen L, Schneider R, Iliopoulos I..
13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2013), 10–13 Nov 2013, Chania, Crete, Greece. [Link] [CONFERENCE]

Interpreting the Omics ‘era’ data
Pavlopoulos GA, Iacucci E, Iliopoulos I, Bagos PG.
Multimedia Services in Intelligent Environments (Smart Innovation, Systems and Technologies, vol. 25). Springer-Verlag, Germany. 2013; pp. 79–100. DOI: 10.1007/978-3-319-00375-7_6 [Springer] [BOOK CHAPTER]

A bioinformatics e-dating story: Computational prediction and prioritization of receptor-ligand pairs
Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Sifrim A, Moreau Y.
BMC Bioinformatics. 2012;13(Suppl 18):A7. [ARTICLE]

Annotate-it: A Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, Sakai R, Pavlopoulos GA, Devriendt K, Vermeesch JR, Moreau Y, Aerts J.
Genome Med. 2012;4:73. doi:10.1186/gm374. PMID:23013645. [ARTICLE]

ReLiance: A machine learning and literature-based prioritization of receptor-ligand pairings
Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Moreau Y.
Bioinformatics. 2012 Sep 15;28(18):i569-i574. PMID:22962483. [ARTICLE]

Human Gene Correlation Analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes
Michalopoulos I, Pavlopoulos GA, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S.
BMC Res Notes. 2012;5:265. PMID:22672625. [ARTICLE]

Arena3D: Visualizing time-driven phenotypic differences in biological systems
Secrier M, Pavlopoulos GA, Aerts J, Schneider R.
BMC Bioinformatics. 2012 Mar 22;13:45. PMID:22439608. [ARTICLE]

Caipirini: Using gene sets to search literature
Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R.
BioData Min. 2012 Feb 1;5(1):1. PMID:22297131. [ARTICLE]

A simple genetic algorithm for cancer biomarker mining
Popovic D, Sifrim A, Pavlopoulos GA, Moreau Y, De Moor B..
PRIB 2012, Lecture Notes in Computer Science, 7632, pp. 222-232, Springer (2012). [Link] [CONFERENCE]

Visualizing High Dimensional Datasets Using Parallel Coordinates: Application to Gene Prioritization
Boogaerts T, Tranchevent LC, Pavlopoulos GA, Aerts J, Vandewalle J..
12th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2012), Nov. 2012, pp. 1-7, Larnaca, Cyprus. [Link] [CONFERENCE]

Mining cell cycle-related literature using support vector machines
Soldatos TG, Pavlopoulos GA.
SETN 2012, Lecture Notes in Computer Science, 7297, pp. 278-284. Springer, Heidelberg (2012). [Link] [CONFERENCE]

Towards better prioritization of epigenetically modified DNA regions
Iacucci E, Popovic D, Pavlopoulos GA, Tranchevent LC, De Moor B, Moreau Y..
SETN 2012, Lecture Notes in Computer Science, 7297, pp. 270-277. Springer, Heidelberg (2012). [Link] [CONFERENCE]

Which algorithm is better for predicting protein complexes?
Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis SD, Schneider R, Kossida S.
BMC Res Notes. 2011 Dec 20;4:549. PMID:22185599. [ARTICLE]

Analyzing protein–protein interaction networks with web tools
Moschopoulos CN, Pavlopoulos GA, Likothanassis SD, Kossida S.
Curr Bioinform. 2011;6(4):389-397. [ARTICLE]

Medusa: A tool for exploring and clustering biological networks
Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J.
BMC Res Notes. 2011 Oct 6;4:384. PMID:21978489. [ARTICLE]

Using graph theory to analyze biological networks
Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R.
BioData Min. 2011 Apr 28;4:10. PMID:21527005. [ARTICLE]

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques
Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ.
Database (Oxford). 2010 Aug 5;2010:baq030. PMID:20689020. [ARTICLE]

A reference guide for tree analysis and visualization
Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R.
BioData Min. 2010 Feb 22;3(1):1. PMID:20175922. [ARTICLE]

LAITOR—Literature Assistant for Identification of Terms co-Occurrences and Relationships: Plant-adaptative responses as a model
Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM.
BMC Bioinformatics. 2010 Feb 1;11:70. PMID:20122157. [ARTICLE]

jClust: A clustering and visualization toolkit
Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S.
Bioinformatics. 2009 Aug 1;25(15):1994-1996. doi:10.1093/bioinformatics/btp314. PMID:19454618. [ARTICLE]

OnTheFly: A tool for automated document-based text annotation, data linking and network generation
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R.
Bioinformatics. 2009 Apr 1;25(7):977-978. doi:10.1093/bioinformatics/btp091. PMID:19223449. [ARTICLE]

GIBA: A clustering tool for detecting protein complexes
Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S.
BMC Bioinformatics. 2009 Jun 16;10(Suppl 6):S11. PMID:19534736. [ARTICLE]

Arena3D: Visualization of biological networks in 3D
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R.
BMC Syst Biol. 2008 Nov 28;2:104. PMID:19040715. [ARTICLE]

A survey of visualization tools for biological network analysis
Pavlopoulos GA, Wegener AL, Schneider R.
BioData Min. 2008 Nov 28;1(1):12. PMID:19040716. [ARTICLE]

An enhanced Markov clustering method for detecting protein complexes
Moschopoulos CN, Pavlopoulos GA, Likothanassis SD, Kossida S..
8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2008), 8–10 October 2008, Athens, Greece. [Link] [CONFERENCE]