Dr. Manuel Gil

Projects

• Inferring the molecular evolutionary history with multiple-character indels: from theory to practice / Co-project leader / ongoing
• Novel Markov chain Monte Carlo algorithms for Bayesian inference / Team member / completed
• Computational literature-based natural product drug discovery / Project leader / completed
• Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Co-project leader / completed
• Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data / Team member / completed

Publications

Articles in scientific journal, peer-reviewed

• Seppey, M., Iglhaut, C., Gil, M., & Anisimova, M. (2025). Impact of phylogenetic method choice on Iindel analyses in HIV-1 subtype B. Genome Biology and Evolution, 17(6), evaf119. https://doi.org/10.1093/gbe/evaf119
• Jowkar, G., Pečerska, J., Gil, M., & Anisimova, M. (2024). Single-character insertion–deletion model preserves long indels in ancestral sequence reconstruction. BMC Bioinformatics, 25(370). https://doi.org/10.1186/s12859-024-05986-1
• Jowkar, G., Pecerska, J., Maiolo, M., Gil, M., & Anisimova, M. (2022). ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process. Systematic Biology, 72(2), 307–318. https://doi.org/10.1093/sysbio/syac050
• Lardos, A., Aghaebrahimian, A., Koroleva, A., Sidorova, J., Wolfram, E., Anisimova, M., & Gil, M. (2022). Computational literature-based discovery for natural products research : current state and future prospects. Frontiers in Bioinformatics, 2(827207). https://doi.org/10.3389/fbinf.2022.827207
• Maiolo, M., Gatti, L., Frei, D., Leidi, T., Gil, M., & Anisimova, M. (2021). ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics, 22(1), 518. https://doi.org/10.1186/s12859-021-04442-8
• Liang, S., Stockinger, K., de Farias, T. M., Anisimova, M., & Gil, M. (2021). Querying knowledge graphs in natural language. Journal of Big Data, 8(3). https://doi.org/10.1186/s40537-020-00383-w
• Maiolo, M., Ulzega, S., Gil, M., & Anisimova, M. (2020). Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform. NAR Genomics and Bioinformatics, 2(4), lqaa092. https://doi.org/10.1093/nargab/lqaa092
• Sima, A.-C., Mendes de Farias, T., Zbinden, E., Anisimova, M., Gil, M., Stockinger, H., Stockinger, K., Robinson-Rechavi, M., & Dessimoz, C. (2019). Enabling semantic queries across federated bioinformatics databases. Database: The Journal of Biological Databases and Curation, 2019(baz106). https://doi.org/10.1093/database/baz106
• Maiolo, M., Zhang, X., Gil, M., & Anisimova, M. (2018). Progressive multiple sequence alignment with indel evolution. BMC Bioinformatics, 19(331). https://doi.org/10.1186/s12859-018-2357-1
• Tan, G., Gil, M., Löytynoja, A. P., Goldman, N., & Dessimoz, C. (2015). Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proceedings of the National Academy of Sciences of the United States of America, 112(2), E99–E100. https://doi.org/10.1073/pnas.1417526112
• Anisimova, M., Gatti, L., Gil, M., & Maiolo, M. (2015). The SIB Swiss Institute of Bioinformatics’ resources : focus on curated databases. Nucleic Acids Research, 44(D1), D27–D37. https://doi.org/10.1093/nar/gkv1310
• Tan, G., Muffato, M., Ledergerber, C., Herrero, J., Goldman, N., Gil, M., & Dessimoz, C. (2015). Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology, 64(5), 778–791. https://doi.org/10.1093/sysbio/syv033

Book chapters, peer-reviewed

• Sima, A.-C., Stockinger, K., de Farias, T. M., & Gil, M. (2019). Semantic integration and enrichment of heterogeneous biological databases. In M. Anisimova (Ed.), Evolutionary genomics : statistical and computational methods (pp. 655–690). Springer. https://doi.org/10.1007/978-1-4939-9074-0_22
• Gil, M., & Anisimova, M. (2015). Methodologies for phylogenetic inference. In Encyclopedia of life sciences. Wiley. https://doi.org/10.1002/9780470015902.a0025545

Written conference contributions, peer-reviewed

• Aghaebrahimian, A., Anisimova, M., & Gil, M. (2022). Ontology-aware biomedical relation extraction [Conference paper]. In P. Sojka, A. Horák, I. Kopeček, & K. Pala (Eds.), Text, Speech, and Dialogue (pp. 160–171). Springer. https://doi.org/10.1007/978-3-031-16270-1_14
• Koroleva, A., Anisimova, M., & Gil, M. (2020). Towards creating a new triple store for literature-based discovery [Conference paper]. In W. Lu & K. Q. Zhu (Eds.), Trends and Applications in Knowledge Discovery and Data Mining. PAKDD 2020 (pp. 41–50). Springer. https://doi.org/10.1007/978-3-030-60470-7_5

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