Dr. Manuel Gil

Leitungsfunktion

• Studiengangleitung MSc Vertiefung in Applied Computational Life Sciences
• Leitung Head of Biomedical String Analysis

Tätigkeit an der ZHAW als

Senior researcher and lecturer
Head of Biomedical String Analysis
Program director MSc specialisation in Applied Computational Life Sciences

mgilsci.github.io

Lehrtätigkeit in der Weiterbildung

CAS Digital Basics for Life Sciences

Arbeits- und Forschungsschwerpunkte, Spezialkenntnisse

Algorithms, Computational Science, String Analysis, Computational Genomics, Computational Linguistics, Semantic Integration, Inferential Statistics

Aus- und Fortbildung

Dr. sc. ETH

Beruflicher Werdegang

2013—2015 Senior Postdoc, Prof. C. v. Mering’s group, Institute of Molecular Life Sciences, Uni Zurich
2012—2013 Visiting Scientist, Prof. A. v. Haeseler’s group, Center for Integrative Bioinformatics, Vienna
2011—2012 Lecturer, ETH Zurich
2010—2012 Postdoc, Prof. G. Gonnet’s group, ETH Zurich

Mitglied in Netzwerken

• Swiss Institute of Bioinformatics

• Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Co-ProjektleiterIn / Projekt laufend
• Computational literature-based natural product drug discovery / 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

• 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

• 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

Gil M (2014) Fast and accurate estimation of the covariance between pairwise maximum likelihood distances, PeerJ, 2:e583

Gil M*, Zanetti MS*, Zoller S, Anisimova M (2013) CodonPhyML: Fast maximum likelihood phylogeny estimation under codon substitution models, Mol. Biol. Evol., 30(6):1270–80

Altenhoff A, Gil M, Gonnet GH, Dessimoz C (2013) Inferring hierarchical orthologous groups from orthologous gene pairs, PLoS ONE, 8(1):e53786

Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes, Systematic Biology, 60(5):685–699

Dessimoz C*, Gil M* (2010) Phylogenetic assessment of alignments reveals neglected tree signal in gaps, Genome Biology, 11:R37

Dessimoz C*, Gil M* (2008) Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise, BMC Evol Biol, 8:179

Fultona DC, Stettler M, Mettler T, Vaughan CK, Li J, Francisco P, Gil M, Reinhold H, Eicke S, Messerli G, Dorkin G, Halliday K, Smith AM, Smith SM, Zeeman SC, BETA-AMYLASE 4 (2008) A Noncatalytic protein that is required for starch breakdown, acts upstream of three active Beta-amylases in Arabidopsis chloroplasts, Plant Cell, 20:1040–1058

Dessimoz C, Gil M, Schneider A, Gonnet GH (2006) Fast estimation of the difference of PAM/JTT evolutionary distances in triplets of homologous sequences, BMC Bioinformatics, 7:529

Gil M, Gonnet GH, Petersen W (2006) A repetition test for random number generators, Monte Carlo Meth Appl, 12(5):385–393

Gil M, Dessimoz C, Gonnet GH (2005) A dimensionless fit measure for phylogenetic distance trees, J Bioinform Comput Biol, 3(6):1429–1440

Dessimoz C, Cannarozzi G, Gil M, Margadant M, Roth A, Schneider A, Gonnet GH, (2005) OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: introduction and first achievements, RECOMB 2005, LNBI 3687:61–72

Hofstoetter C, Gil M, Eng K, Indiveri G, Mintz M, Kramer J, Verschure PFMJ (2005) The Cerebellum Chip: an analog VLSI implementation of a cerebellar model of classical conditioning, NIPS, 17:577–584

Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C (2014) Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment, in: Multiple Sequence Alignment Methods (Editor: Russell D), Methods in Molecular Biology, Springer Humana, Vol 1079: 59–73

Gil M, Gonnet GH (2009) Phylogenetic tree building methods, in: Bioinformatics - A Swiss Perspective (Editors:Appel R, Feytmans E, Swiss Institute of Bioinformatics, Lausanne), World Scientific

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