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Ilias Georgakopoulos-Soares

  • Assistant Professor of Pharmacology & Toxicology
  • Interdisciplinary Life Sciences Graduate Programs

Dr. Georgakopoulos-Soares is an Assistant Professor in the College of Pharmacy at The University of Texas at Austin. His research integrates bioinformatics and AI-driven computational biology to investigate the evolutionary forces shaping genomes, non-canonical DNA structures, and human health and disease, with a particular emphasis on cancer.

The lab's cancer research program spans multiple areas, including gastrointestinal and pediatric malignancies. A major focus is the development non-invasive approaches through liquid biopsies, that the group is leveraging to create new methods for early stage cancer detection and identification of neoantigens to develop new cancer therapies in close collaboration with clinical and industry partners. Additionally, mechanistic studies are underway to gain fundamental insights into cancer biology and shape how we approach cancer risk assessment and treatment selection.

Other current projects include the identification of species-specific DNA sequences across hundreds of thousands of genomes and their functional significance in evolution and species differentiation and the characterization of non-canonical DNA structures across large-scale genomic datasets and their effect on gene regulation and genome stability. The group also creates and maintains a variety of freely accessible software tools and databases that serve as resources for the scientific community to accelerate genomic discovery.

Profile image of Ilias Georgakopoulos-Soares
ilias@austin.utexas.edu

Biography

  • Imperial College London, UK BSc 2014 Biological Sciences
  • University Of Cambridge, UK PhD 2019 Biological Sciences
  • National Technical University of Athens, GR BEng & MEng 2022 Mechanical Engineering
  • Postdoc: 2019-2022 University of California, San Francisco, USA
  • Assistant Professor: 2022-2025 Penn State College of Medicine

Research

Dr. Georgakopoulos-Soares is an Assistant Professor in the College of Pharmacy at The University of Texas at Austin. His research integrates bioinformatics and AI-driven computational biology to investigate the evolutionary forces shaping genomes, non-canonical DNA structures, and human health and disease, with a particular emphasis on cancer.

The lab's cancer research program spans multiple areas, including gastrointestinal and pediatric malignancies. A major focus is the development non-invasive approaches through liquid biopsies, that the group is leveraging to create new methods for early stage cancer detection and identification of neoantigens to develop new cancer therapies in close collaboration with clinical and industry partners. Additionally, mechanistic studies are underway to gain fundamental insights into cancer biology and shape how we approach cancer risk assessment and treatment selection.

Other current projects include the identification of species-specific DNA sequences across hundreds of thousands of genomes and their functional significance in evolution and species differentiation and the characterization of non-canonical DNA structures across large-scale genomic datasets and their effect on gene regulation and genome stability. The group also creates and maintains a variety of freely accessible software tools and databases that serve as resources for the scientific community to accelerate genomic discovery.

Research Areas

  • Computational Medicine or Computational Science
  • AI for Health or Computational Science
  • Biochemistry

Fields of Interest

  • Genomics, Genetics and Development
  • Molecular Biology, Genetics & Genomics
  • Bioinformatics & Computational Biology
  • Statistical/Machine Learning
  • Evolutionary Biology
  • Health & Medicine

Centers and Institutes

  • Oden Institute for Computational Engineering and Sciences

Publications

    • Parada, Guillermo E; Munita, Roberto; Georgakopoulos-Soares, Ilias; Fernandes, Hugo JR; Kedlian, Veronika R; Metzakopian, Emmanouil; Andres, Maria Estela; Miska, Eric A; Hemberg, Martin; (2021). MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biology 22.0(1) : 43 . BioMed Central London.
    • Georgakopoulos-Soares, Ilias; Jain, Naman; Gray, Jesse M; Hemberg, Martin; (2017). MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. Bioinformatics 33.0(1) : 137-138 . Oxford University Press.
    • Roufas, Constantinos; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2021). Distinct genomic features across cytolytic subgroups in skin melanoma. Cancer Immunology, Immunotherapy 70.0(11) : 3137-3154 . Springer Berlin Heidelberg Berlin/Heidelberg.
    • Chartoumpekis, Dionysios V; Ziros, Panos G; Georgakopoulos-Soares, Ilias; Smith, Adam AT; Marques, Ana Claudia; Ibberson, Mark; A. Kopp, Peter; Habeos, Ioannis; Trougakos, Ioannis P; Khoo, Nicholas KH; (2020). The transcriptomic response of the murine thyroid gland to iodide overload and the role of the Nrf2 antioxidant system. Antioxidants 9.0(9) : 884 . MDPI.
    • Georgakopoulos-Soares, Ilias; Morganella, Sandro; Jain, Naman; Hemberg, Martin; Nik-Zainal, Serena; (2018). Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis. Genome research 28.0(9) : 1264-1271 . Cold Spring Harbor Lab.
    • Petljak, Mia; Alexandrov, Ludmil B; Brammeld, Jonathan S; Price, Stacey; Wedge, David C; Grossmann, Sebastian; Dawson, Kevin J; Ju, Young Seok; Iorio, Francesco; Tubio, Jose MC; (2019). Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis. Cell 176.0(6) : 1282-1294. e20 . Elsevier.
    • Georgakopoulos-Soares, Ilias; Koh, Gene; Momen, Sophie E; Jiricny, Josef; Hemberg, Martin; Nik-Zainal, Serena; (2020). Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nature communications 11.0(1) : 1980 . Nature Publishing Group UK London.
    • Degasperi, Andrea; Amarante, Tauanne Dias; Czarnecki, Jan; Shooter, Scott; Zou, Xueqing; Glodzik, Dominik; Morganella, Sandro; Nanda, Arjun S; Badja, Cherif; Koh, Gene; (2020). A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies. Nature cancer 1.0(2) : 249-263 . Nature Publishing Group US New York.
    • Georgakopoulos-Soares, Ilias; Yizhar-Barnea, Ofer; Mouratidis, Ioannis; Hemberg, Martin; Ahituv, Nadav; (2021). Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. Genome Biology 22.0(1) : 245 . BioMed Central London.
    • Georgakopoulos-Soares, Ilias; Chartoumpekis, Dionysios V; Kyriazopoulou, Venetsana; Zaravinos, Apostolos; (2020). EMT factors and metabolic pathways in cancer. Frontiers in oncology 10.0 : 499 . Frontiers Media SA.
    • Gordon, M Grace; Inoue, Fumitaka; Martin, Beth; Schubach, Max; Agarwal, Vikram; Whalen, Sean; Feng, Shiyun; Zhao, Jingjing; Ashuach, Tal; Ziffra, Ryan; (2020). lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols 15.0(8) : 2387-2412 . Nature Publishing Group UK London.
    • Georgakopoulos-Soares, Ilias; Parada, Guillermo E; Wong, Hei Yuen; Medhi, Ragini; Furlan, Giulia; Munita, Roberto; Miska, Eric A; Kwok, Chun Kit; Hemberg, Martin; (2022). Alternative splicing modulation by G-quadruplexes. Nature Communications 13.0(1) : 2404 . Nature Publishing Group UK London.
    • Zaravinos, Apostolos; Roufas, Constantinos; Georgakopoulos-Soares, Ilias; (2020). 867 Distinct genomic features across cytolytic subgroups in skin melanoma. . BMJ Specialist Journals.
    • Georgakopoulos-Soares, Ilias; Mouratidis, Ioannis; Parada, Guillermo E; Matharu, Navneet; Hemberg, Martin; Ahituv, Nadav; (2021). Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences. Nucleic acids research 49.0(1) : e4-e4 . Oxford University Press.
    • Parada González, Guillermo Eduardo; Munita Robert, Roberto Andrés; Georgakopoulos-Soares, Ilias; Fernandes, Hugo JR; Kedlian, Veronika R; Metzakopian, Emmanouil; Andrés Coke, María Estela; Miska, Eric A; Hemberg, Martin; (2021). MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development.
    • Roufas, Constantinos; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2021). Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis. NAR cancer 3.0(1) : zcab005 . Oxford University Press.
    • Ushiki, Aki; Zhang, Yichi; Xiong, Chenling; Zhao, Jingjing; Georgakopoulos-Soares, Ilias; Kane, Lauren; Jamieson, Kirsty; Bamshad, Michael J; Nickerson, Deborah A; 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 12.0(1) : 2282 . Nature Publishing Group UK London.
    • Georgakopoulos-Soares, Ilias; Yizhar-Barnea, Ofer; Mouratidis, Ioannis; Chan, Candace SY; Patsakis, Michail; Nayak, Akshatha; Bradley, Rachael; Mahajan, Mayank; Sims, Jasmine; Cintron, Dianne Laboy; (2025). Leveraging sequences missing from the human genome to diagnose cancer. Communications Medicine 5.0(1) : 363 . Nature Publishing Group UK London.
    • Georgakopoulos-Soares, I; Chartoumpekis, DV; Kyriazopoulou, V; Zaravinos, A; (2020). EMT factors and metabolic pathways in Cancer. Front Oncol. 2020; 10: 499. . Epub 2020/04/23. doi: 10.3389/fonc. 2020.00499. pubMed pMID: 32318352.
    • Gordon, M Grace; Inoue, Fumitaka; Martin, Beth; Schubach, Max; Agarwal, Vikram; Whalen, Sean; Feng, Shiyun; Zhao, Jingjing; Ashuach, Tal; Ziffra, Ryan; (2021). Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols 16.0(7) : 3736.
    • Georgakopoulos-Soares, Ilias; Victorino, Jesus; Parada, Guillermo E; Agarwal, Vikram; Zhao, Jingjing; Wong, Hei Yuen; Umar, Mubarak Ishaq; Elor, Orry; Muhwezi, Allan; An, Joon-Yong; (2022). High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genomics 2.0(4) . Elsevier.
    • Georgakopoulos-Soares, Ilias; Parada, Guillermo E; Hemberg, Martin; (2022). Secondary structures in RNA synthesis, splicing and translation. Computational and structural biotechnology journal 20.0 : 2871-2884 . Elsevier.
    • Georgakopoulos-Soares, Ilias; Chan, Candace SY; Ahituv, Nadav; Hemberg, Martin; (2022). High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome biology 23.0(1) : 159 . BioMed Central London.
    • Georgakopoulos-Soares, Ilias; Chan, Candace SY; Ahituv, Nadav; Hemberg, Martin; (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 23.0(1) : 164 . BioMed Central London.
    • Georgakopoulos-Soares, Ilias; (2022). On the study of the laser absorption coefficient by rough surfaces using Perlin noise.
    • Georgakopoulos-Soares, Ilias; Papazoglou, Emmanouil L; Markopoulos, Angelos P; (2023). On the use of the Perlin noise function to calculate the laser absorption coefficient by rough surfaces. Simulation Modelling Practice and Theory 124.0 : 102722 . Elsevier.
    • Liu, Zhe; Georgakopoulos-Soares, Ilias; Ahituv, Nadav; Wong, Ka-Chun; (2023). Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights. Life Sciences 316.0 : 121413 . Pergamon.
    • Gordon, Wei E; Baek, Seungbyn; Nguyen, Hai P; Kuo, Yien-Ming; Bradley, Rachael; Galazyuk, Alex; Lee, Insuk; Ingala, Melissa R; Simmons, Nancy B; Schountz, Tony; (2023). Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas. BioRxiv : 2023.02. 12.528204 . Cold Spring Harbor Laboratory.
    • Moeckel, Camille; Zaravinos, Apostolos; Georgakopoulos-Soares, Ilias; (2023). Strand asymmetries across genomic processes. Computational and Structural Biotechnology Journal 21.0 : 2036-2047 . Elsevier.
    • Kanellou, Peggy; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2023). Deregulated gene expression profiles and regulatory networks in adult and pediatric RUNX1/RUNX1T1-positive AML patients. Cancers 15.0(6) : 1795 . MDPI.
    • Barnea, Ofer Yizhar; Georgakopoulos-Soares, Ilias; Ahituv, Nadav; Chapman, Jocelyn; Hemberg, Martin; Mouratidis, Ioannis; Syrigos, Konstantinos; Syrigos, Nikolaos; Vathiotis, Ioannis; Mahajan, Mayank; (2023). Leveraging sequences missing from the human genome to detect cancer. Cancer Research 83.0(7_Supplement) : 991-991 . The American Association for Cancer Research.
    • Moeckel, Camille; Bakhl, Katrina; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2023). The efficacy of tumor mutation burden as a biomarker of response to immune checkpoint inhibitors. International journal of molecular sciences 24.0(7) : 6710 . MDPI.
    • Georgakopoulos-Soares, Ilias; Deng, Chengyu; Agarwal, Vikram; Chan, Candace SY; Zhao, Jingjing; Inoue, Fumitaka; Ahituv, Nadav; (2023). Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nature communications 14.0(1) : 2333 . Nature Publishing Group UK London.
    • Mouratidis, Ioannis; Chan, Candace SY; Chantzi, Nikol; Tsiatsianis, Georgios Christos; Hemberg, Martin; Ahituv, Nadav; Georgakopoulos-Soares, Ilias; (2023). Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR Genomics and Bioinformatics 5.0(2) : lqad039 . Oxford University Press.
    • Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2023). Mutational signatures and immune response in cancer. Frontiers in Genetics 14.0 : 1215326 . Frontiers Media SA.
    • Montgomery, Austin; Tsiatsianis, Georgios Christos; Mouratidis, Ioannis; Chan, Candace SY; Athanasiou, Maria; Papanastasiou, Anastasios D; Kantere, Verena; Syrigos, Nikos; Vathiotis, Ioannis; Syrigos, Konstantinos; (2024). Utilizing nullomers in cell-free RNA for early cancer detection. Cancer gene therapy 31.0(6) : 861-870 . Nature Publishing Group US New York.
    • Mouratidis, Ioannis; Chantzi, Nikol; Khan, Umair; Konnaris, Maxwell A; Chan, Candace SY; Mareboina, Manvita; Moeckel, Camille; Georgakopoulos-Soares, Ilias; (2023). Frequentmers-a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis. BMC genomics 24.0(1) : 768 . BioMed Central London.
    • Chantzi, Nikol; Mareboina, Manvita; Konnaris, Maxwell A; Montgomery, Austin; Patsakis, Michail; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; (2024). The determinants of the rarity of nucleic and peptide short sequences in nature. NAR Genomics and Bioinformatics 6.0(2) : lqae029 . Oxford University Press.
    • Chartoumpekis, Dionysios; Georgakopoulos-Soares, Ilias; (2023). FRI022 The Stress-Response Pathways Of NRF2 And Notch Are Upregulated In The Adipocytes But Not In The Immune Cells Of Obese Subjects Adipose Tissue. Journal of the Endocrine Society 7.0(Supplement_1) : bvad114. 033 . Oxford University Press US.
    • Georgakopoulos-Soares, Ilias; Papazoglou, Emmanouil L; Karmiris-Obratański, Panagiotis; Karkalos, Nikolaos E; Markopoulos, Angelos P; (2023). Surface antibacterial properties enhanced through engineered textures and surface roughness: A review. Colloids and Surfaces B: Biointerfaces 231.0 : 113584 . Elsevier.
    • Panagiotou, E; Livanou, ME; Montgomery, A; Mastrogeorgiou, M; Moeckel, C; Syrigos, N; Mouratidis, I; Charpidou, A; Georgakopoulos-Soares, I; Vathiotis, I; (2023). 2007P Real-world (rw) outcomes to chemoimmunotherapy and biomarker analysis in extensive-stage small cell lung cancer (ES SCLC). Annals of Oncology 34.0 : S1069 . Elsevier.
    • Tsiatsianis, Georgios Christos; Chan, Candace SY; Mouratidis, Ioannis; Chantzi, Nikol; Tsiatsiani, Anna Maria; Yee, Nelson S; Zaravinos, Apostolos; Kantere, Verena; Georgakopoulos-Soares, Ilias; (2024). Peptide absent sequences emerging in human cancers. European Journal of Cancer 196.0 : 113421 . Pergamon.
    • Livanou, Maria Effrosyni; Syrigos, Nikolaos K; Montgomery, Austin; Moeckel, Camille; Panagiotou, Emmanouil; Charpidou, Andriani; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; Vathiotis, Ioannis A; (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 186.0 : 107424 . Elsevier.
    • Mouratidis, Ioannis; Baltoumas, Fotis A; Chantzi, Nikol; Patsakis, Michail; Chan, Candace SY; Montgomery, Austin; Konnaris, Maxwell A; Aplakidou, Eleni; Georgakopoulos, George C; Das, Anshuman; (2024). kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species. Computational and structural biotechnology journal 23.0 : 1919-1928 . Elsevier.
    • Zhao, Jingjing; Baltoumas, Fotis A; Konnaris, Maxwell A; Mouratidis, Ioannis; Liu, Zhe; Sims, Jasmine; Agarwal, Vikram; Pavlopoulos, Georgios A; Georgakopoulos-Soares, Ilias; Ahituv, Nadav; (2025). MPRAbase a Massively Parallel Reporter Assay database. Genome Research : gr. 280387.124 . Cold Spring Harbor Lab.
    • Panagiotou, Emmanouil; Vathiotis, Ioannis A; Montgomery, Austin; Moeckel, Camille; Livanou, Maria Effrosyni; Mastrogeorgiou, Michail; Evangelou, Georgios; Charpidou, Andriani; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; (2023). Real-world survival outcomes to first-line chemoimmunotherapy and biomarker analysis in extensive-stage small-cell lung cancer.
    • Koh, Gene Ching Chiek; Boushaki, Soraya; Zhao, Salome Jingchen; Pregnall, Andrew Marcel; Sadiyah, Firas; Badja, Cherif; Memari, Yasin; Georgakopoulos-Soares, Ilias; Nik-Zainal, Serena; (2024). The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells. Nature Genetics 56.0(1) : 23-26 . Nature Publishing Group US New York.
    • Ziros, Panos G; Chartoumpekis, Dionysios V; Georgakopoulos-Soares, Ilias; Psarias, Georgios; Sykiotis, Gerasimos P; (2024). Transcriptomic profiling of the response to excess iodide in Keap1 hypomorphic mice reveals new gene-environment interactions in thyroid homeostasis. Redox biology 69.0 : 102978 . Elsevier.
    • Mouratidis, Ioannis; Konnaris, Maxwell A; Chantzi, Nikol; Chan, Candace SY; Montgomery, Austin; Baltoumas, Fotis A; Patsakis, Michail; Mareboina, Manvita; Pavlopoulos, Georgios A; Chartoumpekis, Dionysios V; (2023). Nucleic quasi-primes: identification of the shortest unique oligonucleotide sequences in a species. bioRxiv : 2023.12. 12.571240 . Cold Spring Harbor Laboratory.
    • Gordon, Wei E; Baek, Seungbyn; Nguyen, Hai P; Kuo, Yien-Ming; Bradley, Rachael; Fong, Sarah L; Kim, Nayeon; Galazyuk, Alex; Lee, Insuk; Ingala, Melissa R; (2024). Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications 15.0(1) : 12 . Nature Publishing Group UK London.
    • Akter, Runa; Tasneem, Faria; Das, Shuvo; Soma, Mahfuza Afroz; Georgakopoulos-Soares, Ilias; Juthi, Rifat Tasnim; Sazed, Saiful Arefeen; (2024). Approaches of dengue control: vaccine strategies and future aspects. Frontiers in immunology 15.0 : 1362780 . Frontiers Media SA.
    • Kosicki, Michael; Cintrón, Dianne Laboy; Page, Nicholas F; Georgakopoulos-Soares, Ilias; Akiyama, Jennifer A; Plajzer-Frick, Ingrid; Novak, Catherine S; Kato, Momoe; Hunter, Riana D; von Maydell, Kianna; (2024). Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity. BioRxiv.
    • Koutras, Angelos; Sirinian, Chaido; Bogri, Olga; Nifora, Martha; Theakou, Maria; Degn, Soren; Mouratidis, Ioannis; Chaniotis, Dimitrios; Peroukidis, Stavros; Georgakopoulos-Soares, Ilias; (2024). Abstract PO4-26-03: Collagen deposition in the breast cancer microenvironment correlates with ER-positive, Histological Grade I and low proliferation tumors. Cancer Research 84.0(9_Supplement) : PO4-26-03-PO4-26-03 . The American Association for Cancer Research.
    • Aplakidou, Eleni; Vergoulidis, Nikolaos; Chasapi, Maria; Venetsianou, Nefeli K; Kokoli, Maria; Panagiotopoulou, Eleni; Iliopoulos, Ioannis; Karatzas, Evangelos; Pafilis, Evangelos; Georgakopoulos-Soares, Ilias; (2024). Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal 23.0 : 2011.
    • Moeckel, Camille; Mouratidis, Ioannis; Chantzi, Nikol; Uzun, Yasin; Georgakopoulos‐Soares, Ilias; (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 46.0(7) : 2300210.
    • Mareboina, Manvita; Bakhl, Katrina; Agioti, Stephanie; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2024). Comprehensive Analysis of Granzymes and Perforin Family Genes in Pan-Cancer.
    • Madej, Marcin; KARKALOS, EK; KARMIRIS-OBRATAŃSKI, P; GEORGAKOPOULOS-SOARES, Ilias; MARKOPOULOS, PA; (2024). An experimental investigation into tribological behaviour of additively manufactured biocompatible Ti-6Al-4V alloy. Materials Research Proceedings 41.0 . Materials Research Forum LLC.
    • Moeckel, Camille; Mareboina, Manvita; Konnaris, Maxwell A; Chan, Candace SY; Mouratidis, Ioannis; Montgomery, Austin; Chantzi, Nikol; Pavlopoulos, Georgios A; Georgakopoulos-Soares, Ilias; (2024). A survey of k-mer methods and applications in bioinformatics. Computational and Structural Biotechnology Journal 23.0 : 2289-2303 . Elsevier.
    • Mareboina, Manvita; Deng, Elen; Mouratidis, Ioannis; Yee, Nelson S; Pitteloud, Nelly; Georgakopoulos-Soares, Ilias; Chartoumpekis, Dionysios V; (2024). A review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomes. Molecular metabolism 87.0 : 101987 . Elsevier.
    • Chantzi, Nikol; Nayak, Akshatha; Baltoumas, Fotis A; Aplakidou, Eleni; Liew, Shiau Wei; Galuh, Jesslyn Elvaretta; Patsakis, Michail; Moeckel, Camille; Mouratidis, Ioannis; Sazed, Saiful Arefeen; (2024). Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life. bioRxiv : 2024.07. 09.602008 . Cold Spring Harbor Laboratory.
    • Chantzi, Nikol; Chan, Candace SY; Patsakis, Michail; Nayak, Akshatha; Montgomery, Austin; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; (2025). Ribosomal DNA arrays are the most H-DNA rich element in the human genome. NAR Genomics and Bioinformatics 7.0(1) : lqaf012 . Oxford University Press.
    • Ahituv, Nadav; YIZHAR-BARNEA, Ofer; GEORGAKOPOUOS-SOARES, Ilias; MOURATIDIS, Ioannis; HEMBERG, Martin; (2024). Compositions comprising nullomers and methods of using the same for cancer detection and diagnosis. . US Patent App. 18/558,992.
    • Rigopoulos, Christos; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2024). A multi-omics analysis of an exhausted T cells’ molecular signature in pan-cancer. Journal of Personalized Medicine 14.0(7) : 765 . MDPI.
    • Chantzi, Nikol; Georgakopoulos-Soares, Ilias; (2024). The repertoire of short tandem repeats across the tree of life. bioRxiv : 2024.08. 08.607201 . Cold Spring Harbor Laboratory.
    • Moeckel, Camille; Chartoumpekis, Dionysios; Ziros, Panos; Georgakopoulos-Soares, Ilias; Sykiotis, Gerasimos; (2024). Very low rates of thyroid function testing in human studies evaluating basal metabolic rate. Endocrine Abstracts 101.0 . Bioscientifica.
    • Chantzi, Nikol; Moeckel, Camille; Chan, Candace S Y; Nayak, Akshatha; Wang, Guliang; Mouratidis, Ioannis; Chartoumpekis, Dionysios; Vasquez, Karen M; Georgakopoulos-Soares, Ilias; (2024). Characterization of hairpin loops and cruciforms across 118,065 genomes spanning the tree of life. bioRxiv : 2024.09. 29.615628 . Cold Spring Harbor Laboratory.
    • Yee, Nelson S; Ma, Fenglong; Georgakopoulos-Soares, Ilias; (2023). Machine Intelligence in Pancreatic Cancer. Handbook of Cancer and Immunology : 1-29 . Springer International Publishing Cham.
    • Patsakis, Michail; Provatas, Kimonas; Baltoumas, Fotis A; Chantzi, Nikol; Mouratidis, Ioannis; Pavlopoulos, Georgios A; Georgakopoulos-Soares, Ilias; (2025). MAFin: motif detection in multiple alignment files. Bioinformatics 41.0(4) : btaf125 . Oxford University Press.
    • Chantzi N, Mouratidis I, Georgakopoulos-Soares I. Zimin patterns in genomes. PLOS Computational Biology. 2026 Feb 9;22(2):e1013909.
    • Provatas, Kimonas; Chantzi, Nikol; Patsakis, Michail; Nayak, Akshatha; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; (2024). Microsatellites explorer: A database of short tandem repeats across genomes. Computational and Structural Biotechnology Journal 23.0 : 3817-3826 . Elsevier.
    • Provatas, Kimonas; Chantzi, Nikol; Amptazi, Nafsika; Patsakis, Michail; Nayak, Akshatha; Mouratidis, Ioannis; Zaravinos, Apostolos; Pavlopoulos, Georgios A; Georgakopoulos-Soares, Ilias; (2025). invertiaDB: a database of inverted repeats across organismal genomes. Nucleic acids research 53.0(8) : gkaf329 . Oxford University Press.
    • Patsakis, Michail; Provatas, Kimonas; Karatzikos, Aris; Koilakos, Charalampos; Mouratidis, Ioannis; Georgakopoulos-Soares, Ilias; (2025). MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files. BMC bioinformatics 26.0(1) : 142 . BioMed Central London.
    • Chan, Candace SY; Mouratidis, Ioannis; Montgomery, Austin; Tsiatsianis, Georgios Christos; Chantzi, Nikol; Hemberg, Martin; Ahituv, Nadav; Georgakopoulos-Soares, Ilias; (2025). The topography of nullomer-emerging mutations and their relevance to human disease. Computational and Structural Biotechnology Journal 30.0 : 1-11 . Elsevier.
    • Mouratidis, Ioannis; Konnaris, Maxwell A; Chantzi, Nikol; Chan, Candace SY; Patsakis, Michail; Provatas, Kimonas; Montgomery, Austin; Baltoumas, Fotis A; Sha, Congzhou M; Mareboina, Manvita; (2025). Identification of the shortest species-specific oligonucleotide sequences. Genome research 35.0(2) : 279-295 . Cold Spring Harbor Lab.
    • Agir, Nora; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2025). A Multi-Omics Analysis of a Mitophagy-Related Signature in Pan-Cancer. International journal of molecular sciences 26.0(2) : 448 . MDPI.
    • Agarwal, Vikram; Inoue, Fumitaka; Schubach, Max; Penzar, Dmitry; Martin, Beth K; Dash, Pyaree Mohan; Keukeleire, Pia; Zhang, Zicong; Sohota, Ajuni; Zhao, Jingjing; (2025). Massively parallel characterization of transcriptional regulatory elements. Nature 639.0(8054) : 411-420 . Nature Publishing Group UK London.
    • Mareboina, Manvita; Bakhl, Katrina; Agioti, Stephanie; Yee, Nelson S; Georgakopoulos-Soares, Ilias; Zaravinos, Apostolos; (2025). Comprehensive Analysis of Granzymes and Perforin Family Genes in Multiple Cancers. Biomedicines 13.0(2) : 408.
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    • Bochalis E, Dereki I, Wang G, Sgourou A, Vasquez KM, Georgakopoulos-Soares I. Non-B DNA structures and their contributions to genetic diversity, aging, and disease. Nucleic Acids Research. 2026 Feb 27;54(4):gkag084.
    • Gkoris M, Georgakopoulos-Soares I, Zaravinos A. Single-Cell Mapping Reveals MIF-Centered Immunoregulatory Networks in Colorectal Cancer. International Journal of Molecular Sciences. 2026 Feb 3;27(3):1496.
    • Sha CM, Patsakis M, Mouratidis I, Wei X, Chung T, Kovac J, Georgakopoulos-Soares I. Doing more with less: Genomic quasi-G-primes differentiate septic from healthy patients. PloS one. 2026 Feb 6;21(2):e0341828.
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    • Vryza P, Georgakopoulos-Soares I, Zaravinos A. Predicting skin melanoma progression via LAG-3, TIGIT and HAVCR2. Functional & Integrative Genomics. 2026 Feb 26;26(1):53.
    • Provatas KA, Georgakopoulos-Soares I. BEDCrypt: Privacy-preserving interval analytics with homomorphic encryption. arXiv preprint arXiv:2602.21994. 2026 Feb 25.
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