Embedded Files
- 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 Research 2025 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. 2023 October 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.2023.1157956 PMID: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.2023.01.013 PMID: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.2022.101418 PMID: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/vbac036 PMID: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/microorganisms10020293 PMID: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/lqab090 PMID: 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.2021.746203 PMID: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/biom11081245 PMID: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 Research 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 Research, 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 LINK View-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/lqaa005 PMID: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:10.1155/2017/1278932 PMID: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/s13104-017-2607-8 PMID: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.aah4043 PMID: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
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