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.

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

Machine Intelligence in Pancreatic Cancer

Nelson Yee, Fenglong Ma, Ilias Georgakopoulos-Soares, Springer Nature

Very low rates of thyroid function testing in human studies evaluating basal metabolic rate

Camille Moeckel, Dionysios Chartoumpekis, Panos Ziros, Ilias Georgakopoulos-Soares, Gerasimos Sykiotis,

Microsatellites Explorer: A Database of Short Tandem Repeats Across Genomes

Ilias Georgakopoulos-Soares,

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

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

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 review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomes

Manvita Mareboina, Elen Deng, Ioannis Mouratidis, Nelson S. Yee, Nelly Pitteloud, Ilias Georgakopoulos-Soares, Dionysios V. Chartoumpekis, 2024, Molecular Metabolism

A Multi-Omics Analysis of an Exhausted T Cells’ Molecular Signature in Pan-Cancer

Christos Rigopoulos, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, 2024, Journal of Personalized Medicine

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

Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity.

M Kosicki, D Cintrón, N Page, Ilias Georgakopoulos-Soares, J Akiyama, I Plajzer-Frick, C Novak, M Kato, R Hunter, K von Maydell, S Barton, P Godfrey, E Beckman, S Sanders, L Pennacchio, N Ahituv, 2024, bioRxiv : the preprint server for 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 Amarante, Jan Czarnecki, Scott Shooter, Xueqing Zou, Dominik Glodzik, Sandro Morganella, Arjun Nanda, Cherif Badja, Gene Koh, Sophie Momen, Ilias Georgakopoulos-Soares, João 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

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

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

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