Ilias Georgakopoulos-Soares
Assistant Professor
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
Links
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
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
Massively parallel characterization of transcriptional regulatory elements
Vikram Agarwal, Fumitaka Inoue, Max Schubach, Dmitry Penzar, Beth K. Martin, Pyaree Mohan Dash, Pia Keukeleire, Zicong Zhang, Ajuni Sohota, Jingjing Zhao, Ilias Georgakopoulos-Soares, William S. Noble, Galip Gürkan Yardımcı, Ivan V. Kulakovskiy, Martin Kircher, Jay Shendure, Nadav Ahituv, 2025, Nature on p. 411-420
Ribosomal DNA arrays are the most H-DNA rich element in the human genome
Nikol Chantzi, Candace S.Y. Chan, Michail Patsakis, Akshatha Nayak, Austin Montgomery, Ioannis Mouratidis, Ilias Georgakopoulos-Soares, 2025, NAR Genomics and Bioinformatics
Characterization of Exhausted T Cell Signatures in Pan-Cancer Settings
Rifat Tasnim Juthi, Saiful Arefeen Sazed, Manvita Mareboina, Apostolos Zaravinos, Ilias Georgakopoulos-Soares, 2025, International Journal of Molecular Sciences
Comprehensive Analysis of Granzymes and Perforin Family Genes in Multiple Cancers
Manvita Mareboina, Katrina Bakhl, Stephanie Agioti, Nelson S. Yee, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2025, Biomedicines
The topography of nullomer-emerging mutations and their relevance to human disease
Candace S.Y. Chan, Ioannis Mouratidis, Austin Montgomery, Georgios Christos Tsiatsianis, Nikol Chantzi, Martin Hemberg, Nadav Ahituv, Ilias Georgakopoulos-Soares, 2025, Computational and Structural Biotechnology Journal on p. 1-11
A Multi-Omics Analysis of a Mitophagy-Related Signature in Pan-Cancer
Nora Agir, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2025, International Journal of Molecular Sciences
Identification of the shortest species-specific oligonucleotide sequences
Ioannis Mouratidis, Maxwell A. Konnaris, Nikol Chantzi, Candace S.Y. Chan, Michail Patsakis, Kimonas Provatas, Austin Montgomery, Fotis A. Baltoumas, Congzhou M. Sha, Manvita Mareboina, Georgios A. Pavlopoulos, Dionysios V. Chartoumpekis, Ilias Georgakopoulos-Soares, 2025, Genome Research on p. 279-295
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
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
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
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
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
High-throughput characterization of the role of non-B DNA motifs on promoter function
Ilias Georgakopoulos-Soares, J Victorino, GE Parada, V Agarwal, J Zhao, HY Wong, MI Umar, O Elor, A Muhwezi, JY An, SJ Sanders, CK Kwok, F Inoue, M Hemberg, N Ahituv, 2022, Cell Genomics
News Articles Featuring Ilias Georgakopoulos-Soares
Dec 07, 2023
Penn State researchers announce new comprehensive -Omics database
A group of Penn State scientists have announced kmerDB, an extensive catalogue of sequence information representing all domains of life.
Full Article
Apr 17, 2023
Structured Nucleic Acids Day, Robert Simpson and Sons Lecture set for April 18
A half-day symposium on structured (noncanonical) nucleic acids will be held on Tuesday, April 18, in Foster Auditorium, Paterno Library, Penn State University Park.
Full Article