Dr. Manuel Gil

Dr. Manuel Gil
ZHAW
Life Sciences und Facility Management
FG Biomedical String Analysis
Schloss 1
8820 Wädenswil
Persönliches Profil
Leitungsfunktion
- Studiengangleitung MSc Vertiefung in Applied Computational Life Sciences
- Leitung Head of Biomedical String Analysis
Tätigkeit an der ZHAW
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
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.
Systematic Biology.
Verfügbar unter: https://doi.org/10.1093/sysbio/syac050
-
Lardos, Andreas; Aghaebrahimian, Ahmad; Koroleva, Anna; Sidorova, Julia; Wolfram, Evelyn; Anisimova, Maria; Gil, Manuel,
2022.
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.
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.
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
Publikationen vor Tätigkeit an der 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