The Georgakopoulos-Soares lab uses bioinformatic and genomics approaches across basic science research problems and in translational medicine.

 

We are particularly interested in gene regulation and in developing new methods for the diagnosis, monitoring, and treatment of human diseases.

Disease Detection

We are interested in the development of novel algorithms and methods for the diagnosis, monitoring, and treatment of human diseases including bacterial and viral infections and of aging-associated diseases including neurodegenerative diseases and cancer.

Publications
  • Mouratidis, I., Chan, C. S., Chantzi, N., Tsiatsianis, G. C., Hemberg, M., Ahituv, N., & Georgakopoulos-Soares, I. (2023). Quasi-prime peptides: identification of the shortest peptide sequences unique to a species. NAR Genomics and Bioinformatics, 5(2), lqad039.

Nullomers

Nullomers are short DNA sequences absent from a genome. We are interested in characterizing them, understanding their functions and using them as biomarkers. As an extension, we are also interested in mathematical and algorithmic implementations of new concepts, such as quasi-primes, the shortest sequences unique to an organism.

Publications
  • Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Hemberg M, Ahituv N. Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. Genome Biol. 2021 Aug 25;22(1):245. doi: 10.1186/s13059-021-02459-z. PubMed PMID: 34433494, PMCID: PMC8386077
  • Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Bradley R, Easterlin R, Chan C, Chen E, Witte J, Hemberg M, Ahituv N. Leveraging sequences missing from the human genome to diagnose cancer. medRxiv 2021.08.15.21261805; doi: https://doi.org/10.1101/2021.08.15.21261805

Cis-regulatory Logic

The gene regulatory code is only partially understood. We are interested in developing methods that enable us to understand cis-regulatory rules, predict non-coding sequence activity and link these to human diseases.

Publications
  • Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C. S., Zhao, J., Inoue, F., & Ahituv, N. (2023). Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nature communications, 14(1), 2333.

Secondary Structures

DNA and RNA secondary structures have an impact on a plethora of biological processes and have been associated with increased mutability. Examples of secondary structures include long range interactions, hairpins, triple-stranded DNA, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. We are interested in understanding their regulatory roles and too study them in relationship to mutability and evolution.

 

 

 

 

 

 

 

 

Publications
  • Georgakopoulos-Soares I, Chan CSY, Ahituv N, Hemberg M. High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol. 2022 Jul 18;23(1):159. doi: 10.1186/s13059-022-02727-6. Review. Erratum in: Genome Biol. 2022 Jul 27;23(1):164. PubMed [citation] PMID: 35851062, PMCID: PMC9290270
  • Georgakopoulos-Soares, I., Parada, G., Wong, H., Medhi, R., Furlan, G., Munita, R., Miska, E., Kwok, C., & Hemberg, M. (2022). Alternative splicing modulation by G-quadruplexes. Nature communications, 13(1), 2404.
  • Georgakopoulos-Soares, Ilias et al. “Secondary structures in RNA synthesis, splicing and translation.” Computational and structural biotechnology journal vol. 20 2871-2884. 27 May. 2022, doi:10.1016/j.csbj.2022.05.041
  • Georgakopoulos-Soares I, Victorino J, Parada GE, Agarwal V, Zhao J, Wong HY, Umar MI, Elor O, Muhwezi A, An JY, Sanders SJ, Kwok CK, Inoue F, Hemberg M, Ahituv N. High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genom. 2022 Apr 13;2(4). pii: 100111. doi: 10.1016/j.xgen.2022.100111. Epub 2022 Mar 15. PubMed [citation] PMID: 35573091, PMCID: PMC9105345

Cancer Genomics and Transcriptomics

We are studying various aspects of cancer biology including the determinants of mutagenesis in cancer genomes, transcriptomic changes associated with cancer, and the interplay between the tumor microenvironment and the immune system.

 

 

 

Publications
  • Georgakopoulos-Soares I, Morganella S, Jain N, Hemberg M, Nik-Zainal S. Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis. Genome Res. 2018 Sep;28(9):1264-1271. doi: 10.1101/gr.231688.117. Epub 2018 Aug 13. PMID: 30104284; PMCID: PMC6120622.
  • Georgakopoulos-Soares, I., Koh, G., Momen, S.E. et al. Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nat Commun 11, 1980 (2020). https://doi.org/10.1038/s41467-020-15901-w
  • Constantinos Roufas, Ilias Georgakopoulos-Soares, Apostolos Zaravinos, Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis, NAR Cancer, Volume 3, Issue 1, March 2021, https://doi.org/10.1093/na/zcab00
  • Roufas, C., Georgakopoulos-Soares, I. & Zaravinos, A. Distinct genomic features across cytolytic subgroups in skin melanoma. Cancer Immunol Immunother 70, 3137–3154 (2021). https://doi.org/10.1007/s00262-021-02918-3

Software and Methods Development

We are interested in the development of new software and computational methods for high-throughput data.

Publications
  • Georgakopoulos-Soares I, Mouratidis I, Parada GE, Matharu N, Hemberg M, Ahituv N. Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences. Nucleic Acids Res. 2021 Jan 11;49(1):e4. doi: 10.1093/nar/gkaa1052. PubMed PMID: 33211865
  • Georgakopoulos-Soares I, Jain N, Gray JM, Hemberg M. MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments. Bioinformatics. 2017 Jan 1;33(1):137-138. doi: 10.1093/bioinformatics/btw584. Epub 2016 Sep 6. PubMed PMID: 27605100