Ilias Georgakopoulos-Soares, PhD - Penn State Cancer Institute
Researcher Profile
Ilias Georgakopoulos-Soares, PhD
Assistant Professor, Department of Biochemistry and Molecular Biology
One Health Microbiome Center
One Health Microbiome Center
Scientific Program:Cancer Control
Research Interests
Dr. Ilias Georgakopoulos-Soares implements bioinformatic and genomics approaches across basic science research problems and in translational medicine.
- DNA
- Neoplasms
- Genome
- Genes
- RNA
- Regulator Genes
- Mutation
- Mutagenesis
- Transcription Factors
- G-Quadruplexes
- Colorectal Neoplasms
- Nucleotide Motifs
Recent Publications
2024
Rigopoulos, C, Georgakopoulos-Soares, I & Zaravinos, A 2024, 'A Multi-Omics Analysis of an Exhausted T Cells’ Molecular Signature in Pan-Cancer', Journal of Personalized Medicine, vol. 14, no. 7, 765. https://doi.org/10.3390/jpm14070765
Mareboina, M, Deng, E, Mouratidis, I, Yee, NS, Pitteloud, N, Georgakopoulos-Soares, I & Chartoumpekis, DV 2024, 'A review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomes', Molecular Metabolism, vol. 87, 101987. https://doi.org/10.1016/j.molmet.2024.101987
Moeckel, C, Mareboina, M, Konnaris, MA, Chan, CSY, Mouratidis, I, Montgomery, A, Chantzi, N, Pavlopoulos, GA & Georgakopoulos-Soares, I 2024, 'A survey of k-mer methods and applications in bioinformatics', Computational and Structural Biotechnology Journal, vol. 23, pp. 2289-2303. https://doi.org/10.1016/j.csbj.2024.05.025
Moeckel, C, Mouratidis, I, Chantzi, N, Uzun, Y & Georgakopoulos-Soares, I 2024, 'Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights', BioEssays, vol. 46, no. 7, 2300210. https://doi.org/10.1002/bies.202300210
Madej, M, Karkalos, NE, Karmiris-Obratanski, P, Papazoglou, EL, Georgakopoulos-Soares, I & Markopoulos, AP 2024, An experimental investigation into tribological behaviour of additively manufactured biocompatible Ti-6Al-4V alloy. in AC Araujo, A Cantarel, F Chabert, A Korycki, P Olivier & F Schmidt (eds), Material Forming, ESAFORM 2024. Materials Research Proceedings, vol. 41, Association of American Publishers, pp. 174-182, 27th International ESAFORM Conference on Material Forming, ESAFORM 2024, Toulouse, France, 4/24/24. https://doi.org/10.21741/9781644903131-19
Akter, R, Tasneem, F, Das, S, Soma, MA, Georgakopoulos-Soares, I, Juthi, RT & Sazed, SA 2024, 'Approaches of dengue control: vaccine strategies and future aspects', Frontiers in immunology, vol. 15, 1362780. https://doi.org/10.3389/fimmu.2024.1362780
Gordon, WE, Baek, S, Nguyen, HP, Kuo, YM, Bradley, R, Fong, SL, Kim, N, Galazyuk, A, Lee, I, Ingala, MR, Simmons, NB, Schountz, T, Cooper, LN, Georgakopoulos-Soares, I, Hemberg, M & Ahituv, N 2024, 'Correction to: Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas (Nature Communications, (2024), 15, 1, (12), 10.1038/s41467-023-44186-y)', Nature communications, vol. 15, no. 1, 1777. https://doi.org/10.1038/s41467-024-44937-5
Gordon, WE, Baek, S, Nguyen, HP, Kuo, YM, Bradley, R, Fong, SL, Kim, N, Galazyuk, A, Lee, I, Ingala, MR, Simmons, NB, Schountz, T, Cooper, LN, Georgakopoulos-Soares, I, Hemberg, M & Ahituv, N 2024, 'Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas', Nature communications, vol. 15, no. 1, 12. https://doi.org/10.1038/s41467-023-44186-y
Tsiatsianis, GC, Chan, CSY, Mouratidis, I, Chantzi, N, Tsiatsiani, AM, Yee, NS, Zaravinos, A, Kantere, V & Georgakopoulos-Soares, I 2024, 'Peptide absent sequences emerging in human cancers', European Journal of Cancer, vol. 196, 113421. https://doi.org/10.1016/j.ejca.2023.113421
Chantzi, N, Mareboina, M, Konnaris, MA, Montgomery, A, Patsakis, M, Mouratidis, I & Georgakopoulos-Soares, I 2024, 'The determinants of the rarity of nucleic and peptide short sequences in nature', NAR Genomics and Bioinformatics, vol. 6, no. 2, lqae029. https://doi.org/10.1093/nargab/lqae029
Ziros, PG, Chartoumpekis, DV, Georgakopoulos-Soares, I, Psarias, G & Sykiotis, GP 2024, 'Transcriptomic profiling of the response to excess iodide in Keap1 hypomorphic mice reveals new gene-environment interactions in thyroid homeostasis', Redox Biology, vol. 69, 102978. https://doi.org/10.1016/j.redox.2023.102978
Montgomery, A, Tsiatsianis, GC, Mouratidis, I, Chan, CSY, Athanasiou, M, Papanastasiou, AD, Kantere, V, Syrigos, N, Vathiotis, I, Syrigos, K, Yee, NS & Georgakopoulos-Soares, I 2024, 'Utilizing nullomers in cell-free RNA for early cancer detection', Cancer gene therapy, vol. 31, no. 6, pp. 861-870. https://doi.org/10.1038/s41417-024-00741-3
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 2024, 'Visualizing metagenomic and metatranscriptomic data: A comprehensive review', Computational and Structural Biotechnology Journal, vol. 23, pp. 2011-2033. https://doi.org/10.1016/j.csbj.2024.04.060
Mouratidis, I, Baltoumas, FA, Chantzi, N, Patsakis, M, Chan, CSY, Montgomery, A, Konnaris, MA, Aplakidou, E, Georgakopoulos, GC, Das, A, Chartoumpekis, DV, Kovac, J, Pavlopoulos, GA & Georgakopoulos-Soares, I 2024, 'kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species', Computational and Structural Biotechnology Journal, vol. 23, pp. 1919-1928. https://doi.org/10.1016/j.csbj.2024.04.050
2023
Kanellou, P, Georgakopoulos-Soares, I & Zaravinos, A 2023, 'Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients', Cancers, vol. 15, no. 6, 1795. https://doi.org/10.3390/cancers15061795
Georgakopoulos-Soares, I & Zaravinos, A 2023, 'Editorial: Mutational signatures and immune response in cancer', Frontiers in Genetics, vol. 14, 1215326. https://doi.org/10.3389/fgene.2023.1215326
Livanou, ME, Syrigos, NK, Montgomery, A, Moeckel, C, Panagiotou, E, Charpidou, A, Mouratidis, I, Georgakopoulos-Soares, I & Vathiotis, IA 2023, 'Eligibility for screening with low-dose CT in a real-world cohort of patients with lung cancer in Greece: A brief report', Lung Cancer, vol. 186, 107424. https://doi.org/10.1016/j.lungcan.2023.107424
Mouratidis, I, Chantzi, N, Khan, U, Konnaris, MA, Chan, CSY, Mareboina, M, Moeckel, C & Georgakopoulos-Soares, I 2023, 'Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis', BMC genomics, vol. 24, no. 1, 768. https://doi.org/10.1186/s12864-023-09861-w
Georgakopoulos-Soares, I, Papazoglou, EL & Markopoulos, AP 2023, 'On the use of the Perlin noise function to calculate the laser absorption coefficient by rough surfaces', Simulation Modelling Practice and Theory, vol. 124, 102722. https://doi.org/10.1016/j.simpat.2022.102722
Mouratidis, I, Chan, CSY, Chantzi, N, Tsiatsianis, GC, Hemberg, M, Ahituv, N & Georgakopoulos-Soares, I 2023, 'Quasi-prime peptides: identification of the shortest peptide sequences unique to a species', NAR Genomics and Bioinformatics, vol. 5, no. 2, lqad039. https://doi.org/10.1093/nargab/lqad039
Liu, Z, Georgakopoulos-Soares, I, Ahituv, N & Wong, KC 2023, 'Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights', Life Sciences, vol. 316, 121413. https://doi.org/10.1016/j.lfs.2023.121413
Moeckel, C, Zaravinos, A & Georgakopoulos-Soares, I 2023, 'Strand asymmetries across genomic processes', Computational and Structural Biotechnology Journal, vol. 21, pp. 2036-2047. https://doi.org/10.1016/j.csbj.2023.03.007
Georgakopoulos-Soares, I, Papazoglou, EL, Karmiris-Obratański, P, Karkalos, NE & Markopoulos, AP 2023, 'Surface antibacterial properties enhanced through engineered textures and surface roughness: A review', Colloids and Surfaces B: Biointerfaces, vol. 231, 113584. https://doi.org/10.1016/j.colsurfb.2023.113584
Moeckel, C, Bakhl, K, Georgakopoulos-Soares, I & Zaravinos, A 2023, 'The Efficacy of Tumor Mutation Burden as a Biomarker of Response to Immune Checkpoint Inhibitors', International journal of molecular sciences, vol. 24, no. 7, 6710. https://doi.org/10.3390/ijms24076710
Koh, GCC, Boushaki, S, Zhao, SJ, Pregnall, AM, Sadiyah, F, Badja, C, Memari, Y, Georgakopoulos-Soares, I & Nik-Zainal, S 2024, 'The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells', Nature Genetics, vol. 56, no. 1, pp. 23-26. https://doi.org/10.1038/s41588-023-01602-9
Georgakopoulos-Soares, I, Deng, C, Agarwal, V, Chan, CSY, Zhao, J, Inoue, F & Ahituv, N 2023, 'Transcription factor binding site orientation and order are major drivers of gene regulatory activity', Nature communications, vol. 14, no. 1, 2333. https://doi.org/10.1038/s41467-023-37960-5
2022
Georgakopoulos-Soares, I, Parada, GE, Wong, HY, Medhi, R, Furlan, G, Munita, R, Miska, EA, Kwok, CK & Hemberg, M 2022, 'Alternative splicing modulation by G-quadruplexes', Nature communications, vol. 13, no. 1, 2404. https://doi.org/10.1038/s41467-022-30071-7
Georgakopoulos-Soares, I, Chan, CSY, Ahituv, N & Hemberg, M 2022, 'Author Correction: High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation (Genome Biology, (2022), 23, 1, (159), 10.1186/s13059-022-02727-6)', Genome biology, vol. 23, no. 1, 164. https://doi.org/10.1186/s13059-022-02733-8
Georgakopoulos-Soares, I, Victorino, J, Parada, GE, Agarwal, V, Zhao, J, Wong, HY, Umar, MI, Elor, O, Muhwezi, A, An, JY, Sanders, SJ, Kwok, CK, Inoue, F, Hemberg, M & Ahituv, N 2022, 'High-throughput characterization of the role of non-B DNA motifs on promoter function', Cell Genomics, vol. 2, no. 4, 100111. https://doi.org/10.1016/j.xgen.2022.100111
Georgakopoulos-Soares, I, Chan, CSY, Ahituv, N & Hemberg, M 2022, 'High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation', Genome biology, vol. 23, no. 1, 159. https://doi.org/10.1186/s13059-022-02727-6
Georgakopoulos-Soares, I, Parada, GE & Hemberg, M 2022, 'Secondary structures in RNA synthesis, splicing and translation', Computational and Structural Biotechnology Journal, vol. 20, pp. 2871-2884. https://doi.org/10.1016/j.csbj.2022.05.041
2021
Georgakopoulos-Soares, I, Yizhar-Barnea, O, Mouratidis, I, Hemberg, M & Ahituv, N 2021, 'Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution', Genome biology, vol. 22, no. 1, 245. https://doi.org/10.1186/s13059-021-02459-z
Georgakopoulos-Soares, I, Mouratidis, I, Parada, GE, Matharu, N, Hemberg, M & Ahituv, N 2021, 'Asymmetron: A toolkit for the identification of strand asymmetry patterns in biological sequences', Nucleic acids research, vol. 49, no. 1, pp. E4. https://doi.org/10.1093/nar/gkaa1052
University of Washington Center for Mendelian Genomics 2021, 'Deletion of CTCF sites in the SHH locus alters enhancer–promoter interactions and leads to acheiropodia', Nature communications, vol. 12, no. 1, 2282. https://doi.org/10.1038/s41467-021-22470-z
Roufas, C, Georgakopoulos-Soares, I & Zaravinos, A 2021, 'Distinct genomic features across cytolytic subgroups in skin melanoma', Cancer Immunology, Immunotherapy, vol. 70, no. 11, pp. 3137-3154. https://doi.org/10.1007/s00262-021-02918-3
Parada, GE, Munita, R, Georgakopoulos-Soares, I, Fernandes, HJR, Kedlian, VR, Metzakopian, E, Andres, ME, Miska, EA & Hemberg, M 2021, 'MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development', Genome biology, vol. 22, no. 1, 43. https://doi.org/10.1186/s13059-020-02246-2
Roufas, C, Georgakopoulos-Soares, I & Zaravinos, A 2021, 'Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis', NAR Cancer, vol. 3, no. 1, zcab005. https://doi.org/10.1093/narcan/zcab005
2020
Degasperi, A, Amarante, TD, Czarnecki, J, Shooter, S, Zou, X, Glodzik, D, Morganella, S, Nanda, AS, Badja, C, Koh, G, Momen, SE, Georgakopoulos-Soares, I, Dias, JML, Young, J, Memari, Y, Davies, H & Nik-Zainal, S 2020, 'A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies', Nature Cancer, vol. 1, no. 2, pp. 249-263. https://doi.org/10.1038/s43018-020-0027-5
Georgakopoulos-Soares, I, Chartoumpekis, DV, Kyriazopoulou, V & Zaravinos, A 2020, 'EMT Factors and Metabolic Pathways in Cancer', Frontiers in Oncology, vol. 10, 499. https://doi.org/10.3389/fonc.2020.00499
Degasperi, A, Amarante, TD, Czarnecki, J, Shooter, S, Zou, X, Glodzik, D, Morganella, S, Nanda, AS, Badja, C, Koh, G, Momen, SE, Georgakopoulos-Soares, I, Dias, JML, Young, J, Memari, Y, Davies, H & Nik-Zainal, S 2020, 'Erratum: Author Correction: A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies (Nature cancer (2020) 1 2 (249-263))', Nature Cancer, vol. 1, no. 7, pp. 748. https://doi.org/10.1038/s43018-020-0093-8
Chartoumpekis, DV, Ziros, PG, Georgakopoulos-Soares, I, Smith, AAT, Marques, AC, Ibberson, M, Kopp, PA, Habeos, I, Trougakos, IP, Khoo, NKH & Sykiotis, GP 2020, 'The transcriptomic response of the murine thyroid gland to iodide overload and the role of the nrf2 antioxidant system', Antioxidants, vol. 9, no. 9, 0884, pp. 1-21. https://doi.org/10.3390/antiox9090884
Georgakopoulos-Soares, I, Koh, G, Momen, SE, Jiricny, J, Hemberg, M & Nik-Zainal, S 2020, 'Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts', Nature communications, vol. 11, no. 1, 1980. https://doi.org/10.1038/s41467-020-15901-w
Gordon, MG, Inoue, F, Martin, B, Schubach, M, Agarwal, V, Whalen, S, Feng, S, Zhao, J, Ashuach, T, Ziffra, R, Kreimer, A, Georgakopoulous-Soares, I, Yosef, N, Ye, CJ, Pollard, KS, Shendure, J, Kircher, M & Ahituv, N 2020, 'lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements', Nature Protocols, vol. 15, no. 8, pp. 2387-2412. https://doi.org/10.1038/s41596-020-0333-5