Dr. Manuel Gil

Dr. Manuel Gil
ZHAW
School of Life Sciences and Facility Management
Fachstelle Computational Genomics
Einsiedlerstrasse 31a
8820 Wädenswil
Personal profile
Management role
Programme Director, MSc specialisation in Applied Computational Life Sciences
Position at the ZHAW
Senior researcher and lecturer
Program director MSc specialisation in Applied Computational Life Sciences
Expertise and research interests
Algorithms, Inferential Statistics, Computational Science, Computational Genomics, Stochastic Modeling for Genomic Data, Computational Linguistics
Educational background
Dr. sc. ETH
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
Membership of networks
Projects
- Computational literature-based natural product drug discovery / Project leader / Project ongoing
- Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Team member / Project ongoing
- Radiosands / Team member / Project ongoing
- Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data / Team member / Project ongoing
Publications
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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/10.21256/zhaw-18771
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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/10.21256/zhaw-4775
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Tan, Ge; Muffato, Matthieu; Ledergerber, Christian; Herrero, Javier; Goldman, Nick; Gil, Manuel; Dessimoz, Christophe,
2015.
Systematic biology.
64(5),
pp. 778-791.
Available from: https://doi.org/10.21256/zhaw-4267
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Tan, Ge; Gil, Manuel; Löytynoja, Ari P.; Goldman, Nick; Dessimoz, Christophe,
2015.
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
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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/10.21256/zhaw-3859
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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/10.21256/zhaw-3138
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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
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