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 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,
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
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
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
kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species
I Mouratidis, Fotis A. Baltoumas, Nikol Chantzi, Michail Patsakis, Chan CSY, 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
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
News Articles Featuring Ilias Georgakopoulos-Soares
Dec 07, 2023
Penn State researchers announce new comprehensive -Omics database
A group of Penn State scientists have announced kmerDB, an extensive catalogue of sequence information representing all domains of life.
Full Article
Apr 17, 2023
Structured Nucleic Acids Day, Robert Simpson and Sons Lecture set for April 18
A half-day symposium on structured (noncanonical) nucleic acids will be held on Tuesday, April 18, in Foster Auditorium, Paterno Library, Penn State University Park.
Full Article