Dr. Manuel Gil

Projects

• Computational literature-based natural product drug discovery / Project leader / Project completed
• Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Project co-leader / Project completed
• Radiosands / Team member / Project completed
• Bio-SODA – Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (SNSF NRP 75 "Big Data") / Team member / Project completed

Publications

• Jowkar, Gholamhossein; Pecerska, Julija; Maiolo, Massimo; Gil, Manuel; Anisimova, Maria,

  2022.

  ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process.

  Systematic Biology.

  72(2), pp. 307-318.

  Available from: https://doi.org/10.1093/sysbio/syac050

• Lardos, Andreas; Aghaebrahimian, Ahmad; Koroleva, Anna; Sidorova, Julia; Wolfram, Evelyn; Anisimova, Maria; Gil, Manuel,

  2022.

  Computational literature-based discovery for natural products research : current state and future prospects.

  Frontiers in Bioinformatics.

  2(827207).

  Available from: https://doi.org/10.3389/fbinf.2022.827207

• Maiolo, Massimo; Gatti, Lorenzo; Frei, Diego; Leidi, Tiziano; Gil, Manuel; Anisimova, Maria,

  2021.

  ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process.

  BMC Bioinformatics.

  22(1), pp. 518.

  Available from: https://doi.org/10.1186/s12859-021-04442-8

• Liang, Shiqi; Stockinger, Kurt; de Farias, Tarcisio Mendes; Anisimova, Maria; Gil, Manuel,

  2021.

  Querying knowledge graphs in natural language.

  Journal of Big Data.

  8(3).

  Available from: https://doi.org/10.1186/s40537-020-00383-w

• Maiolo, Massimo; Ulzega, Simone; Gil, Manuel; Anisimova, Maria,

  2020.

  Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform.

  NAR Genomics and Bioinformatics.

  2(4), pp. lqaa092.

  Available from: https://doi.org/10.1093/nargab/lqaa092

• Sima, Ana-Claudia; Mendes de Farias, Tarcisio; Zbinden, Erich; Anisimova, Maria; Gil, Manuel; Stockinger, Heinz; Stockinger, Kurt; Robinson-Rechavi, Marc; Dessimoz, Christophe,

  2019.

  Enabling semantic queries across federated bioinformatics databases.

  Database: The Journal of Biological Databases and Curation.

  2019(baz106).

  Available from: https://doi.org/10.1093/database/baz106

• Maiolo, Massimo; Zhang, Xiaolei; Gil, Manuel; Anisimova, Maria,

  2018.

  Progressive multiple sequence alignment with indel evolution.

  BMC Bioinformatics.

  19(331).

  Available from: https://doi.org/10.1186/s12859-018-2357-1

• Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe,

  2015.

  Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference.

  Systematic Biology.

  64(5), pp. 778-791.

  Available from: https://doi.org/10.1093/sysbio/syv033

• Tan, Ge; Gil, Manuel; Löytynoja, Ari P.; Goldman, Nick; Dessimoz, Christophe,

  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), pp. E99-E100.

  Available from: https://doi.org/10.1073/pnas.1417526112

• Anisimova, Maria; Gatti, Lorenzo; Gil, Manuel; Maiolo, Massimo,

  2015.

  The SIB Swiss Institute of Bioinformatics’ resources : focus on curated databases.

  Nucleic Acids Research.

  44(D1), pp. D27-D37.

  Available from: https://doi.org/10.1093/nar/gkv1310

• Sima, Ana-Claudia; Stockinger, Kurt; de Farias, Tarcisio Mendes; Gil, Manuel,

  2019.

  Semantic integration and enrichment of heterogeneous biological databases

  .

  In:

  Anisimova, Maria, ed.,

  Evolutionary genomics : statistical and computational methods.

  New York:

  Springer.

  pp. 655-690.

  Methods in Molecular Biology ; 1910.

  Available from: https://doi.org/10.1007/978-1-4939-9074-0_22

• Gil, Manuel; Anisimova, Maria,

  2015.

  Methodologies for phylogenetic inference

  .

  In:

  Encyclopedia of life sciences.

  Hoboken:

  Wiley.

  Available from: https://doi.org/10.1002/9780470015902.a0025545

• Aghaebrahimian, Ahmad; Anisimova, Maria; Gil, Manuel,

  2022.

  Ontology-aware biomedical relation extraction [paper].

  In:

  Sojka, Petr; Horák, Aleš; Kopeček, Ivan; Pala, Karel, eds.,

  Text, Speech, and Dialogue.

  25th International Conference on Text, Speech and Dialogue (TSD), Brno, Czech Republic, 6-9 September 2022.

  Cham:

  Springer.

  pp. 160-171.

  Lecture Notes in Computer Science ; 13502.

  Available from: https://doi.org/10.1007/978-3-031-16270-1_14

• Koroleva, Anna; Anisimova, Maria; Gil, Manuel,

  2020.

  Towards creating a new triple store for literature-based discovery [paper].

  In:

  Lu, Wei; Zhu, Kenny Q., eds.,

  Trends and Applications in Knowledge Discovery and Data Mining. PAKDD 2020.

  PAKDD 2020 Workshops, DSFN, GII, BDM, LDRC and LBD, Singapore, 11-14 May 2020.

  Cham:

  Springer.

  pp. 41-50.

  Lecture Notes in Computer Science ; 12237.

  Available from: https://doi.org/10.1007/978-3-030-60470-7_5

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