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.
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Genome Neoplasms Mutation Rna Mutagenesis Regulator Genes Genes Dna Deletion Nucleotide Motifs Embryonic Development Fluorescence Exons Potassium Chloride Circular Dichroism Dna Repair Asymmetry Phenotype Depolarization Mice G Quadruplexes Time Strands Transcription Factors BrainMost Recent Publications
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas
Wei E. Gordon, Seungbyn Baek, Hai P. Nguyen, Yien Ming Kuo, Rachael Bradley, Sarah L. Fong, Nayeon Kim, Alex Galazyuk, Insuk Lee, Melissa R. Ingala, Nancy B. Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv, 2024, Nature Communications
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)
Wei E. Gordon, Seungbyn Baek, Hai P. Nguyen, Yien Ming Kuo, Rachael Bradley, Sarah L. Fong, Nayeon Kim, Alex Galazyuk, Insuk Lee, Melissa R. Ingala, Nancy B. Simmons, Tony Schountz, Lisa Noelle Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg, Nadav Ahituv, 2024, Nature Communications
Transcriptomic profiling of the response to excess iodide in Keap1 hypomorphic mice reveals new gene-environment interactions in thyroid homeostasis
Panos G. Ziros, Dionysios V. Chartoumpekis, Ilias Georgakopoulos-Soares, Georgios Psarias, Gerasimos P. Sykiotis, 2024, Redox Biology
The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells
Gene Ching Chiek Koh, Soraya Boushaki, Salome Jingchen Zhao, Andrew Marcel Pregnall, Firas Sadiyah, Cherif Badja, Yasin Memari, Ilias Georgakopoulos-Soares, Serena Nik-Zainal, 2024, Nature Genetics on p. 23-26
Peptide absent sequences emerging in human cancers
Georgios Christos Tsiatsianis, Candace S.Y. Chan, Ioannis Mouratidis, Nikol Chantzi, Anna Maria Tsiatsiani, Nelson S. Yee, Apostolos Zaravinos, Verena Kantere, Ilias Georgakopoulos-Soares, 2024, European Journal of Cancer
Utilizing nullomers in cell-free RNA for early cancer detection
Austin Montgomery, Georgios Christos Tsiatsianis, Ioannis Mouratidis, Candace S.Y. Chan, Maria Athanasiou, Anastasios D. Papanastasiou, Verena Kantere, Nikos Syrigos, Ioannis Vathiotis, Konstantinos Syrigos, Nelson S. Yee, Ilias Georgakopoulos-Soares, 2024, Cancer Gene Therapy
Eligibility for screening with low-dose CT in a real-world cohort of patients with lung cancer in Greece: A brief report
Maria Effrosyni Livanou, Nikolaos K. Syrigos, Austin Montgomery, Camille Moeckel, Emmanouil Panagiotou, Andriani Charpidou, Ioannis Mouratidis, Ilias Georgakopoulos-Soares, Ioannis A. Vathiotis, 2023, Lung Cancer
Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis
Ioannis Mouratidis, Nikol Chantzi, Umair Khan, Maxwell A. Konnaris, Candace S.Y. Chan, Manvita Mareboina, Camille Moeckel, Ilias Georgakopoulos-Soares, 2023, BMC Genomics
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
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
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 Dias Amarante, Jan Czarnecki, Scott Shooter, Xueqing Zou, Dominik Glodzik, Sandro Morganella, Arjun S. Nanda, Cherif Badja, Gene Koh, Sophie E. Momen, Ilias Georgakopoulos-Soares, João M.L. 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
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-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts
Ilias Georgakopoulos-Soares, Gene Koh, Sophie E. Momen, Josef Jiricny, Martin Hemberg, Serena Nik-Zainal, 2020, 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
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development
Guillermo E. Parada, Roberto Munita, Ilias Georgakopoulos-Soares, Hugo J.R. Fernandes, Veronika R. Kedlian, Emmanouil Metzakopian, Maria Estela Andres, Eric A. Miska, Martin Hemberg, 2021, Genome Biology
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