Dr. Manuel Gil

Netzwerk

Mitglied in Netzwerken

Swiss Institute of Bioinformatics

Projekte

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

Publikationen

• 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), S. 307-318.

  Verfügbar unter: 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).

  Verfügbar unter: 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), S. 518.

  Verfügbar unter: 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).

  Verfügbar unter: 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), S. lqaa092.

  Verfügbar unter: 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).

  Verfügbar unter: 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).

  Verfügbar unter: 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), S. 778-791.

  Verfügbar unter: 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), S. E99-E100.

  Verfügbar unter: 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), S. D27-D37.

  Verfügbar unter: 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, Hrsg.,

  Evolutionary genomics : statistical and computational methods.

  New York:

  Springer.

  S. 655-690.

  Methods in Molecular Biology ; 1910.

  Verfügbar unter: 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.

  Verfügbar unter: 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, Hrsg.,

  Text, Speech, and Dialogue.

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

  Cham:

  Springer.

  S. 160-171.

  Lecture Notes in Computer Science ; 13502.

  Verfügbar unter: 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., Hrsg.,

  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.

  S. 41-50.

  Lecture Notes in Computer Science ; 12237.

  Verfügbar unter: https://doi.org/10.1007/978-3-030-60470-7_5

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