Published

Publications

1. CAnDi: A compendium of anaerobic digestion microbiomes.
   Ghiotto G, Chasapi I, de Bernardini N, Fraulini S, Ndela EO, Baltoumas FA, Treu L, Kyrpides NC, Pavlopoulos GA, Campanaro S.
   Nucleic Acids Res. 2026 Oct 31:gkag1088. doi:10.1093/nar/gkag1088. PMID:42963941. [ARTICLE]

2. ArthroVerse: Mapping protein family diversity across arthropod-associated microbiomes.
   Chasapi IN, Aplakidou E, Chasapi MN, Lamari E, Galaras A, Diplari S, Iliopoulos I, Emiris IZ, Georgakopoulos-Soares I, Patalano S, Stravopodis DJ, Karatzas E, Baltoumas FA, Kyrpides NC, Pavlopoulos GA.
   Nucleic Acids Res. 2026 Oct 27:gkag1067. doi:10.1093/nar/gkag1067. PMID:42934169. [ARTICLE]

3. WasteFams: A database of protein families from global wastewater microbiomes.
   Galaras A, Chasapi IN, Aplakidou E, Chasapi MN, Lamari E, Diplari S, Georgakopoulos-Soares I, Karatzas E, Baltoumas FA, Kyrpides NC, Pavlopoulos GA.
   NAR Genom Bioinform. 2026 Oct 22;8(4):lqag127. doi:10.1093/nargab/lqag127. PMID:42923064. [ARTICLE]

4. ‘Quadrupling’ the protein family space with global metagenomics.
   Aplakidou E, Baltoumas FA, Chasapi MN, Lamari E, Georgakopoulos-Soares I, Karatzas E, Iliopoulos I, Buluç A, Finn RD, Camargo AP, Kyrpides NC, Pavlopoulos GA.
   Nucleic Acids Res. 2026 Sep 22;54(18):gkag938. doi:10.1093/nar/gkag938. PMID:42803189. [ARTICLE]

5. Accelerating inference in genomic and proteomic foundation models via speculative decoding.
   Provatas K, Karatzikos A, Koilakos C, Patsakis M, Tzanakakis A, Nayak A, Pavlopoulos GA, Mouratidis I, Avgoulas EI, Georgakopoulos-Soares I.
   Bioinformatics. 2026 Aug 3;42(8):btag579. doi:10.1093/bioinformatics/btag579. PMID:42536416. [ARTICLE]

6. lncAPNet enables the deciphering of lncRNA–mRNA connections in patient transcriptomic data.
   Vasileiou V, Gavriilidis GI, Zeni PF, Mraz M, Karatzas E, Giakountis A, Pavlopoulos GA, Giannakakis A, Psomopoulos F.
   Bioinform Adv. 2026 Jul 21;6(1):vbag204. doi:10.1093/bioadv/vbag204. PMID:42615010. [ARTICLE]

7. Decoding extremophiles: Insights from bioinformatics, machine learning, and data-driven approaches.
   Chasapi MN, Kontis N, Lehmann R, Tasneem R, Patel NS, Khan SA, Martínez de Morentin X, Chasapi IN, Aplakidou E, Galaras A, Aldakheel L, Su M, Baltoumas FA, Lagani V, Gómez-Cabrero D, Tegner J, Pavlopoulos GA, Rosado AS.
   Brief Bioinform. 2026 May 4;27(3):bbag236. doi:10.1093/bib/bbag236. PMID:42153318. [ARTICLE]

8. nf-core/proteinfamilies: A scalable pipeline for the generation of protein families.
   Karatzas E, Beracochea M, Baltoumas FA, Aplakidou E, Richardson L, Fellows Yates JA, Lundin D, nf-core community, Buluç A, Kyrpides N, Georgakopoulos-Soares I, Pavlopoulos GA, Finn RD.
   GigaScience. 2026 Jan 21;15:giag009. doi:10.1093/gigascience/giag009. PMID:41563008. [ARTICLE]

9. neomerDB: A comprehensive database of neomer biomarkers in cancer.
   Provatas K, Chan CSY, Kerasiotis I, Bochalis E, Nayak A, Zacharia BE, Pavlopoulos GA, Li W, Georgakopoulos-Soares I.
   Database (Oxford). 2026 Jan 15;2026:baag006. doi:10.1093/database/baag006. PMID:41676903. [ARTICLE]

10. Meta-Virus Resource (MetaVR): Expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.
    Fiamenghi MB, Camargo AP, Chasapi IN, Baltoumas F, Roux S, Egorov A, Aplakidou E, Ndela EO, Vasquez YM, Chen I-M, Palaniappan K, Reddy TBK, Mukherjee S, Ivanova N, Schulz F, Woyke T, Eloe-Fadrosh E, Pavlopoulos GA, Kyrpides N.
    Nucleic Acids Res. 2026 Jan 6;54(D1):D801-D812. doi:10.1093/nar/gkaf1283. PMID:41312645. [ARTICLE]

11. B cell tolerance checkpoint function in multiple sclerosis and transient CD52 depletion.
    Alexaki A, Baltoumas F, Tzanetakos D, Zografou C, Dame T, Michaletou C, Kyriakaki G, Vakrakou AG, Anagnostouli M, Karadima G, Tzanoudaki M, Dalakas MC, Stefanis L, Kilidireas K, O'Connor KC, Pavlopoulos GA, Stathopoulos P.
    J Neuroimmunol. 2026 Jan 5;413:578854. doi:10.1016/j.jneuroim.2026.578854. PMID:41505925. [ARTICLE]

12. Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.
    Grigoriadis D, Tsifintaris M, Giannakakis A, Pavlopoulos GA, Perdikopanis N.
    Comput Struct Biotechnol J. 2025;27:4802-4812. doi:10.1016/j.csbj.2025.11.004. PMID:41282419. [ARTICLE]

13. 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 Nov 20:gkaf1174. doi:10.1093/nar/gkaf1174. PMID:41263110. [ARTICLE]

14. 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]

15. 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]

16. 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]

17. 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]

18. 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]

19. 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]

20. 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]

21. 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]

22. 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]

23. 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]

24. 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. PMID:39279874. [ARTICLE]

25. 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. PMID:38840832. [ARTICLE]

26. 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]

27. 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]

28. 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]

29. 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. doi:10.1038/s41586-023-06583-7. PMID:37821698. [ARTICLE]

30. 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]

31. 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]

32. 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]

33. 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]

34. 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]

35. 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, USA. 2022 Nov:1-12. ACM Gordon Bell Prize finalist. [CONFERENCE ARTICLE]

36. 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]

37. 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. PMID:36426957. [ARTICLE]

38. 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]

39. 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]

40. 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]

41. 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]

42. 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]

43. 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(2):293. doi:10.3390/microorganisms10020293. PMID:35208748. [ARTICLE]

44. 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]

45. 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]

46. 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(8):1245. doi:10.3390/biom11081245. PMID:34439912. [ARTICLE]

47. 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]

48. 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]

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

50. 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]

51. 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 J. 2021;26:e943. [ARTICLE]

52. 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]

53. 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]

54. 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]

55. 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]

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

57. PASTIS: Distributed many-to-many protein sequence alignment using sparse matrices.
    Selvitopi O, Ekanayake S, Guidi G, Pavlopoulos GA, Azad A, Buluç A.
    SC20: International Conference for High Performance Computing, Networking, Storage and Analysis. 2020 Nov. [CONFERENCE ARTICLE]

58. 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]

59. 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]

60. 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]

61. 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]

62. 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]

63. 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]

64. 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]

65. 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]

66. 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]

67. 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]

68. 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]

69. 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]

70. 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]

71. 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]

72. 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]

73. 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]

74. 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]

75. 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]

76. 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]

77. 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]

78. 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]

79. 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]

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

81. 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]

82. 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]

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

84. 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), Chania, Crete, Greece. 2013 Nov 10-13. [CONFERENCE ARTICLE]

85. 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]

86. 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]

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

88. 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), Larnaca, Cyprus. 2012 Nov:1-7. [CONFERENCE ARTICLE]

89. 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. Springer. 2012;7632:222-232. [CONFERENCE ARTICLE]

90. 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]

91. 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]

92. 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]

93. 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]

94. Mining cell cycle-related literature using support vector machines.
    Soldatos TG, Pavlopoulos GA.
    SETN 2012, Lecture Notes in Computer Science. Springer, Heidelberg. 2012;7297:278-284. [CONFERENCE ARTICLE]

95. 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. Springer, Heidelberg. 2012;7297:270-277. [CONFERENCE ARTICLE]

96. 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]

97. 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]

98. 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]

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

100. 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]

101. 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]

102. 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]

103. 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]

104. 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]

105. 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]

106. 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]

107. 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]

108. 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]

109. 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]

110. 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), Athens, Greece. 2008 Oct 8-10. [CONFERENCE ARTICLE]