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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Rna Dna Genome Genes Neoplasms Mutation Regulator Genes Mutagenesis Gene Expression Deletion Embryonic Development Methodology Nucleotide Motifs Secondary Structure Gene Regulation Fluorescence Hydrogen G Quadruplexes Exons Circular Dichroism Potassium Chloride Dna Repair Asymmetry Phenotype

Most Recent Publications

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

Quasi-prime peptides: identification of the shortest peptide sequences unique to a species

Ioannis Mouratidis, Candace S.Y. Chan, Nikol Chantzi, Georgios Christos Tsiatsianis, Martin Hemberg, Nadav Ahituv, Ilias Georgakopoulos-Soares, 2023, NAR Genomics and Bioinformatics

The Efficacy of Tumor Mutation Burden as a Biomarker of Response to Immune Checkpoint Inhibitors

Camille Moeckel, Katrina Bakhl, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2023, International Journal of Molecular Sciences

On the use of the Perlin noise function to calculate the laser absorption coefficient by rough surfaces

Ilias Georgakopoulos-Soares, Emmanouil L. Papazoglou, Angelos P. Markopoulos, 2023, Simulation Practice and Theory

Deregulated Gene Expression Profiles and Regulatory Networks in Adult and Pediatric RUNX1/RUNX1T1-Positive AML Patients

Peggy Kanellou, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2023, Cancers

Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights

Zhe Liu, Ilias Georgakopoulos-Soares, Nadav Ahituv, Ka Chun Wong, 2023, Life Sciences

Strand asymmetries across genomic processes

Camille Moeckel, Apostolos Zaravinos, Ilias Georgakopoulos-Soares, 2023, Computational and Structural Biotechnology Journal on p. 2036-2047

Editorial: Mutational signatures and immune response in cancer

Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2023, Frontiers in Genetics

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, (2022), 23, 1, (159), 10.1186/s13059-022-02727-6)

Ilias Georgakopoulos-Soares, Candace S.Y. Chan, Nadav Ahituv, Martin Hemberg, 2022, Genome Biology

High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation

Ilias Georgakopoulos-Soares, Candace S.Y. Chan, Nadav Ahituv, Martin Hemberg, 2022, Genome Biology

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

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

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

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