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 Affiliations
Links
Publication Tags
Rna Dna Genome Mutation Genes Neoplasms Embryonic Development Deletion Secondary Structure Exons Mutagenesis Regulator Genes Proteins Mice Nucleotides G Quadruplexes Brain Loci Skin Gene Acheiropodia Regulation Nucleotide Motifs Enhancer MelanomaMost Recent Publications
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
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
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
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
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution
Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Martin Hemberg, Nadav Ahituv, 2021, Genome Biology
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
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
Distinct genomic features across cytolytic subgroups in skin melanoma
Constantinos Roufas, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2021, Cancer Immunology and Immunotherapy on p. 3137-3154
Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements (Nature Protocols, (2020), 15, 8, (2387-2412), 10.1038/s41596-020-0333-5)
M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S. Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv, 2021, Nature Protocols on p. 3736
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
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
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
Distinct genomic features across cytolytic subgroups in skin melanoma
Constantinos Roufas, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2021, Cancer Immunology and Immunotherapy on p. 3137-3154
MPRAnator: A web-based tool for the design of massively parallel reporter assay experiments
Ilias Georgakopoulos-Soares, Naman Jain, Jesse M. Gray, Martin Hemberg, 2017, Bioinformatics on p. 137-138