Ilias Georgakopoulos-Soares

Assistant Professor

izg5139@psu.edu

Bio & Links
Publications

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

Bioinformatics and Genomics

Microbiome Center

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 Melanoma

Most 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