Dr. Manuel Gil

Work at ZHAW

Management role

• Programme Director, MSc specialisation in Applied Computational Life Sciences
• Head, Head of Biomedical String Analysis

Position at the ZHAW

Researcher and lecturer
Head of Biomedical String Analysis
Program director MSc specialisation Applied Computational Life Sciences

mgilsci.github.io

Education and Continuing education

Expertise and research interests

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

Professional milestones

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

Educational background

Dr. sc. ETH

Membership of networks

Swiss Institute of Bioinformatics

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

Publications before appointment at the ZHAW

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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