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.

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Genome Neoplasms Mutation Rna Mutagenesis Dna Embryonic Development Nucleotide Motifs Deletion Fluorescence Exons Regulator Genes Circular Dichroism Potassium Chloride Dna Repair Asymmetry Depolarization Mice G Quadruplexes Genes Time Strands Brain Rna Seq Phenotype

Most Recent Publications

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

Eleni Aplakidou, Nikolaos Vergoulidis, Maria Chasapi, Nefeli K. Venetsianou, Maria Kokoli, Eleni Panagiotopoulou, Ioannis Iliopoulos, Evangelos Karatzas, Evangelos Pafilis, Ilias Georgakopoulos-Soares, Nikos C. Kyrpides, Georgios A. Pavlopoulos, Fotis A. Baltoumas, 2024, Computational and Structural Biotechnology Journal on p. 2011-2033

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

A survey of k-mer methods and applications in bioinformatics

Camille Moeckel, Manvita Mareboina, Maxwell A. Konnaris, Candace S.Y. Chan, Ioannis Mouratidis, Austin Montgomery, Nikol Chantzi, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares, 2024, Computational and Structural Biotechnology Journal on p. 2289-2303

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

kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species

Ioannis Mouratidis, Fotis A. Baltoumas, Nikol Chantzi, Michail Patsakis, Candace S.Y. Chan, Austin Montgomery, Maxwell A. Konnaris, Eleni Aplakidou, George C. Georgakopoulos, Anshuman Das, Dionysios V. Chartoumpekis, Jasna Kovac, Georgios A. Pavlopoulos, Ilias Georgakopoulos-Soares, 2024, Computational and Structural Biotechnology Journal on p. 1919-1928

The determinants of the rarity of nucleic and peptide short sequences in nature

Nikol Chantzi, Manvita Mareboina, Maxwell A. Konnaris, Austin Montgomery, Michail Patsakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares, 2024, NAR Genomics and Bioinformatics

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

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

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

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