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 Research2025 Apr 22;53(8):gkaf329. doi: 10.1093/nar/gkaf329 PMID:40272360
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 Research, 2025 Apr 22:gr.280387.124. doi: 10.1101/gr.280387.124,PMID:40262894
Multimodal SARS-CoV-2 interactome sketches the virus-host spatial organization Dugied G., Laurent EMN., Mikaël Attia M., Jean-Pascal 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. Communications Biology, 2025 March 26., 8(1), 501. https://doi.org/10.1038/s42003-025-07933-z, PMID:40140549
MAFin: Motif Detection in Multiple Alignment Files Patsakis M., Provatas K., Baltoumas FA, Chantzi N., Mouratidis I., Pavlopoulos GA. Georgakopoulos-Soares I. Bioinformatics(Oxford), 2025 Mar 19:btaf125. doi: 10.1093/bioinformatics/btaf125. PMID:40106711
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 (Oxford), 2025 Feb 8:btaf063. doi: 10.1093/bioinformatics/btaf063. PMID:39921901
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 Research. 14 Feb 2025, 35(2), 279–295, https://doi.org/10.1101/gr.280070.124. PMID:39746719
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 Research,6 Jan 2025, gkae940, https://doi.org/10.1093/nar/gkae940, PMID:39470740
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, Evangelos Andreakos E., Iliopoulos I. Comput Struct Biotechnol J. 2024 Aug 21:23:3247-3253. doi: 10.1016/j.csbj.2024.08.016. eCollection 2024 Dec.PMID:39279874
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. eCollection 2024 Dec.PMID:38840832
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 *co-corresponding
kmerDB: a database encompassing the set of genomic and proteomic sequence information of each species Mouratidis I., Baltoumas FA., Chantzi N., PatsakisM., Chan S.Y, 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 *co-corresponding
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. 2023October 20. ISSN 2001-0370, https://doi.org/10.1016/j.csbj.2023.10.032. PMID:38022693
Unraveling the functional dark matter through global metagenomics. 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. Nature, 2023 Oct;622(7983):594-602. Epub 2023 Oct 11. https://doi.org/10.1038/s41586-023-06583-7, PMID:37821698
NMPFamsDB: A database of novel protein families from microbial metagenomes and metatranscriptomes Baltoumas FA., Karatzas E., Sirui L., Ovchinikov S., Sofianatos Y., I-Min C., Kyrpides NC., Pavlopoulos GA. Nucleic Acids Research 2023 Oct 9:gkad800. doi: 10.1093/nar/gkad800. PMID:37811892
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
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 Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad053, https://doi.org/10.1093/nargab/lqad053 PMID:37260509
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. Frontiers in Bioinformatics, 03 March 2023, Volume 3 -2023, https://doi.org/10.3389/fbinf.2023.1157956PMID:36959975
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, 06 Feb 2023, https://doi.org/10.1016/j.maturitas.2023.01.013PMID:36773500
Drug genetic associations with COVID-19 manifestations: a data mining and network biology approach Charitou T., Kontou PI., Ioannis A Tamposis IA, Pavlopoulos GA., Braliou GG., Bagos PG. The Pharmacogenomics Journal, 28 Sept. 2022. https://doi.org/10.1038/s41397-022-00289-1, PMID:36171417
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. Online ahead of print. PMID: 36426957
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. International Journal of Molecular Sciences, 2022; 23(19):11112. https://doi.org/10.3390/ijms231911112, PMID:36232413
Consolidated variant calling from Whole Exome Sequencing data using three variant callers Verrou KM., Pavlopoulos GA., Moulos P. STAR Protocols (Cell Press), 04 June 2022, Volume 3, Issue 2, https://doi.org/10.1016/j.xpro.2022.101418PMID:35669050
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. Bioinformatics Advances, 13 May 2022;, vbac036, https://doi.org/10.1093/bioadv/vbac036PMID:36699373
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. Molecular Ecology Resources, 2022 May 20. doi: 10.1111/1755-0998.13626. PMID:35593171 - bioRxiv
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; https://doi.org/10.3390/biom12040520 PMID:35454109
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. https://doi.org/10.3390/microorganisms10020293PMID:35208748
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 Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab090, https://doi.org/10.1093/nargab/lqab090PMID: 34632381
Blood transcriptomes of anti-SARS-CoV2 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., 05 October 2021 | https://doi.org/10.3389/fimmu.2021.746203PMID:34675930
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. https://doi.org/10.3390/biom11081245PMID:34439912
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,14 Jul 2021, 10(7), 665; https://doi.org/10.3390/biology10070665 PMID:34356520
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, Chatzopoulou F, Chatzidimitriou D, Panagopoulos P, Lourida P, Argyraki A, Lytras T, Sapounas S, Gerolymatos G, Panagiotakopoulos G, Prezerakos P, Tsiodras S, Sypsa V, Hatzakis A, Anastassopoulou C, Spanakis N, Tsakris A, Dimopoulos MA, Kotanidou A, Sfikakis P, Kollias G, Magiorkinis G, Paraskevis D. mSphere, 2021 Jun 30:e0018021. doi: 10.1128/mSphere.00180-21.PMID:34190583
NORMA-The network makeup artist: a web tool for network annotation visualization Koutrouli M., Karatzas E, Papanikolopoulou K, Pavlopoulos GA. Genomics Proteomics and Bioinformatics, 2021 Jun 22:S1672-0229(21)00130-3. doi: 10.1016/j.gpb.2021.02.005. PMID:34171457
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. Computers in Biology and Medicine, 8 June 2021, 104557, ISSN 0010-4825, https://doi.org/10.1016/j.compbiomed.2021.104557.PMID:34139436
The network analysis profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks Koutrouli M, Theodosiou T, Iliopoulos I, Pavlopoulos GA. EMBnet.journal, v. 26, p. e943, May 2021. ISSN 2226-6089. doi:https://doi.org/10.14806/ej.26.0.943.LINK
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
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
Distinct transcriptional profile of blood mononuclear cells in Behcet'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
The human GPCR signal transduction network Kontou P. Pavlopoulou A, Dimou N, Theodoropoulou M, Braliou G, Tsaousis G, Pavlopoulos GA, Hamodrakas S., Bagos PG Network Modeling Analysis in Health Informatics and Bioinformatics, 14 January 2021, 10:3, doi:10.1007/s13721-020-00278-z LINKView-Only PDF
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 Communications Biology, 2020 Jun 19;3(1):320. doi:10.1038/s42003-020-1047-5.PMID:32561885
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, Karagogeos D, Iliopoulos I NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa005, https://doi.org/10.1093/nargab/lqaa005PMID:33575553
A guide to conquer the biological network era using graph theory Koutrouli M, Karatzas E, Paez-Espino D, Pavlopoulos GA. Front. Bioeng. Biotechnol., 31 January 2020 | https://doi.org/10.3389/fbioe.2020.00034.PMID:32083072
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
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. pii: S0092-8674(19)30781-0. doi: 10.1016/j.cell.2019.07.016 - biorxiv preprint, PMID:31402174
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; Hungate1000 project collaborators, Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. Nature Biotechnology, 2018 Mar 19. doi: 10.1038/nbt.4110.PMID:29553575
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, Volume 7, Issue 4, 1 April 2018, https://doi.org/10.1093/gigascience/giy014,*equal first authors PMID:29648623
HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks. Azad A., Pavlopoulos GA, Ouzounis C., Kyrpides NC, Βuluc A. Nucleic Acids Research, 5 Jan 2018, https://doi.org/10.1093/nar/gkx1313,PMID:29315405
Empirical comparison of visualization tools for larger-scale network analysis Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I. Advances in Bioinformatics, vol. 2017, Article ID 1278932, 8 pages, 2017. doi:10.1155/2017/1278932PMID:28804499
Non-targeted virus sequence discovery pipeline and virus clustering for metagenomic data Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC Nature Protocols 2017 Aug;12(8):1673-1682. doi: 10.1038/nprot.2017.063. PMID:28749930
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 Research Notes, 2017, 10:278, DOI: 10.1186/s13104-017-2607-8PMID:28705239
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, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC Nature Biotechnology,2017 Jun 12. doi: 10.1038/nbt.3886,PMID:28604660
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 Research, 2017 May 17. doi: 10.1093/nar/gkx444.PMID:28520987
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, 20 Jan 2017:Vol. 355, Issue 6322, pp. 294-298, DOI: 10.1126/science.aah4043PMID:28104891
IMG/VR: A database of cultured and uncultured DNA Viruses and Retroviruses Paez-Espino D, Chen AI, 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, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu W, Rivers AR, Ivanova NN, Kyrpides NC Nucleic Acids Research, October 2016, gkw1030v1-gkw1030. PMID:27799466
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
DrugQuest: A text-mining workflow for drug association discovery Papanikolaou N, Pavlopoulos GA, Theodosiou T, Vizirianakis IS, Iliopoulos I. BMC Bioinformatics, June 2016, 17 (Suppl 5):182 DOI 10.1186/s12859-016-1041-6. PMID:27295093
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 in Brief, 2016 Jul 19;8:1036-9. doi: 10.1016/j.dib.2016.07.022. eCollection 2016. PMID:27508260
Network analysis of genes and their association with diseases Kontou PI, Pavlopoulou A., Dimou NL, Pavlopoulos GA, Bagos PG. Gene (Elsevier), Volume 590, Issue 1, 15 September 2016, Pages 68-78, doi:10.1016/j.gene.2016.05.044 PMID:27265032
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. doi: 10.1038/onc.2015.307, PMID:26279300
Visualizing Genome and Systems biology: technologies, tools, implementation techniques and trends, past, present and future Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright A., Iliopoulos I GigaScience, 25 Aug 2015, 4:38 DOI: 10.1186/s13742-015-0077-2 PMID:26309733
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. Bioinformatics and Biology Insights, 25 May 2015, 5;9:75-88. doi: 10.4137/BBI.S12462. eCollection 2015, PMID:25983555
Protein-Protein interaction predictions using text-mining tools Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I. Methods, 2014, Oct 28. pii: S1046-2023(14) 00352-1. doi: 10.1016/j.ymeth.2014.10.026. PMID:25448298
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. *equal first authors Bioinformatics, 2014,doi: 10.1093/bioinformatics/btu524, PMID:25100685
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 July 6:13, doi:10.1186/1756-0381-6-13 PMID:23885890
Meander: visually exploring the structural variome using space-filling curves Pavlopoulos GA, Sifrim A, Sakai R, Kumar PD, Voet T, Moreau Y, Aerts J. Nucleic Acids Research, 2013, 1:9 doi:10.1093/nar/gkt254 PMID:23605045
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 LINK
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 Medicine, 2012, 4:73 doi:10.1186/gm374. PMID:23013645
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 (Oxford), 2012 Sep 15;28(18):i569-i574. PMID:22962483
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 Research Notes, 2012, 5:265. PMID:22672625
Arena3D: Visualizing time-driven phenotypic differences in biological systems Secrier M, Pavlopoulos GA, Aerts J, Schneider R. BMC Bioinformatics, 2012 Mar 22;13(1):45. PMID:22439608
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
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
Analyzing protein-protein interaction networks with web tools Moschopoulos CN, Pavlopoulos GA, Likothanassis SD, Kossida S. Current Bioinformatics, 2011 Dec 6;4:389-397(9). LINK
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(1):384. PMID:21978489
Using graph theory to analyze biological networks Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R. BioData Mining, 2011 Apr 28; 4:10. PMID:21527005
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. PMID:20689020
A reference guide for tree analysis and visualization Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R. BioData Mining 2010 Feb 22;3(1):1. PMID:20175922
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(1):70. PMID:20122157
jClust: A clustering and visualization toolkit Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. Bioinformatics (Oxford), 2009 Aug 1;25(15):1994-6. Epub 2009 May 19. PMID:19454618
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 (Oxford), 2009 Apr 1;25(7):977-8. Epub 2009 Feb 17. PMID:19223449
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
Arena3D: Visualization of Biological Networks in 3D Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. BMC Systems Biology, 2008 Nov 28;2:104. PMID:19040715
A survey of visualization tools for biological network analysis Pavlopoulos GA, Wegener AL, Schneider R. BioData Mining, 2008 Nov 28;1(1):12. PMID:19040716