Ilias Georgakopoulos-Soares

Assistant Professor

Ilias Georgakopoulos-Soares

Research Summary

The development and implementation of new computational methods in genomics and molecular biology, with the aim of identifying genetic biomarkers for the diagnosis, monitoring, and treatment of human diseases, including bacterial and viral infections and of aging-associated diseases including neurodegenerative diseases and cancer.

Huck Graduate Students

Huck Affiliations

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Most Recent Publications

Very low rates of thyroid function testing in human studies evaluating basal metabolic rate

Camille Moeckel, Dionysios Chartoumpekis, Panos Ziros, Ilias Georgakopoulos-Soares, Gerasimos Sykiotis,

Machine Intelligence in Pancreatic Cancer

Nelson Yee, Fenglong Ma, Ilias Georgakopoulos-Soares, Springer Nature

MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files

Michail Patsakis, Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Ioannis Mouratidis, Ilias Georgakopoulos-Soares, 2025, BMC Bioinformatics

Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity

Michael Kosicki, Dianne Laboy Cintrón, Pia Keukeleire, Max Schubach, Nicholas F. Page, Ilias Georgakopoulos-Soares, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Riana D. Hunter, Kianna von Maydell, Sarah Barton, Patrick Godfrey, Erik Beckman, Stephan J. Sanders, Martin Kircher, Len A. Pennacchio, Nadav Ahituv, 2025, Nature Communications

Epitranscriptomics Regulation of CD70, CD80, and TIGIT in Cancer Immunity

Christos Panagiotis Rigopoulos, Marios Gkoris, Ilias Georgakopoulos-Soares, Ioannis Boulalas, Apostolos Zaravinos, 2025, International Journal of Molecular Sciences

Compressive and energy absorption properties of titanium hybrid lattice structures for bioimplant applications fabricated via LPBF

Panagiotis Karmiris-Obratański, Ilias Georgakopoulos-Soares, Kamil Cichocki, Paulina Lisiecka-Graca, Emmanouil L. Papazoglou, 2025, International Journal of Materials in Engineering Applications

invertiaDB: a database of inverted repeats across organismal genomes

Kimonas Provatas, Nikol Chantzi, Nafsika Amptazi, Michail Patsakis, Akshatha Nayak, Ioannis Mouratidis, Apostolos Zaravinos, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares, 2025, Nucleic Acids Research

ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences

Guliang Wang, Ioannis Mouratidis, Kimonas Provatas, Nikol Chantzi, Michail Patsakis, Ilias Georgakopoulos-Soares, Karen M. Vasquez, 2025, Briefings in Bioinformatics

A multi-omics analysis of effector and resting treg cells in pan-cancer

Anna Maria Chalepaki, Marios Gkoris, Irene Chondrou, Malamati Kourti, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2025, Computers in Biology and Medicine

MAFin: Motif detection in multiple alignment files

Michail Patsakis, Kimonas Provatas, Fotis A. Baltoumas, Nikol Chantzi, Ioannis Mouratidis, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares, 2025, Bioinformatics

Most-Cited Papers

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Mia Petljak, Ludmil B. Alexandrov, Jonathan S. Brammeld, Stacey Price, David C. Wedge, Sebastian Grossmann, Kevin J. Dawson, Young Seok Ju, Francesco Iorio, Jose M.C. Tubio, Ching Chiek Koh, Ilias Georgakopoulos-Soares, Bernardo Rodríguez-Martín, Burçak Otlu, Sarah O'Meara, Adam P. Butler, Andrew Menzies, Shriram G. Bhosle, Keiran Raine, David R. Jones, Jon W. Teague, Kathryn Beal, Calli Latimer, Laura O'Neill, Jorge Zamora, Elizabeth Anderson, Nikita Patel, Mark Maddison, Bee Ling Ng, Jennifer Graham, Mathew J. Garnett, Ultan McDermott, Serena Nik-Zainal, Peter J. Campbell, Michael R. Stratton, 2019, Cell on p. 1282-1294.e20

EMT Factors and Metabolic Pathways in Cancer

Ilias Georgakopoulos-Soares, Dionysios V. Chartoumpekis, Venetsana Kyriazopoulou, Apostolos Zaravinos, 2020, Frontiers in Oncology

A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies

Andrea Degasperi, Tauanne Amarante, Jan Czarnecki, Scott Shooter, Xueqing Zou, Dominik Glodzik, Sandro Morganella, Arjun Nanda, Cherif Badja, Gene Koh, Sophie Momen, Ilias Georgakopoulos-Soares, João Dias, Jamie Young, Yasin Memari, Helen Davies, Serena Nik-Zainal, 2020, Nature Cancer on p. 249-263

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

Ilias Georgakopoulos-Soares, Sandro Morganella, Naman Jain, Martin Hemberg, Serena Nik-Zainal, 2018, Genome Research on p. 1264-1271

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulous-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S. Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv, 2020, Nature Protocols on p. 2387-2412

Surface antibacterial properties enhanced through engineered textures and surface roughness: A review

Ilias Georgakopoulos-Soares, Emmanouil L. Papazoglou, Panagiotis Karmiris-Obratański, Nikolaos E. Karkalos, Angelos P. Markopoulos, 2023, Colloids and Surfaces B: Biointerfaces

Alternative splicing modulation by G-quadruplexes

Ilias Georgakopoulos-Soares, Guillermo E. Parada, Hei Yuen Wong, Ragini Medhi, Giulia Furlan, Roberto Munita, Eric A. Miska, Chun Kit Kwok, Martin Hemberg, 2022, Nature Communications

Deletion of CTCF sites in the SHH locus alters enhancer–promoter interactions and leads to acheiropodia

Aki Ushiki, Yichi Zhang, Chenling Xiong, Jingjing Zhao, Ilias Georgakopoulos-Soares, Lauren Kane, Kirsty Jamieson, Michael J. Bamshad, Deborah A. Nickerson, Yin Shen, Laura A. Lettice, Elizabeth Lemos Silveira-Lucas, Florence Petit, Nadav Ahituv, 2021, Nature Communications

Secondary structures in RNA synthesis, splicing and translation

Ilias Georgakopoulos-Soares, Guillermo E. Parada, Martin Hemberg, 2022, Computational and Structural Biotechnology Journal on p. 2871-2884

Transcription factor binding site orientation and order are major drivers of gene regulatory activity

Ilias Georgakopoulos-Soares, Chengyu Deng, Vikram Agarwal, Candace S.Y. Chan, Jingjing Zhao, Fumitaka Inoue, Nadav Ahituv, 2023, Nature Communications