Prof. Dr. Maria Anisimova
Prof. Dr. Maria Anisimova
ZHAW
Life Sciences und Facility Management
FS Bioinformatics
Schloss
8820 Wädenswil
Netzwerk
Mitglied in Netzwerken
- PhD Network in Data Science
- European COST Action BM1405 "Non-globular proteins - from sequence to structure, function & application in molecular physiopathology"
- Swiss Institute of Bioinformatics
- REFRACT MSCA RISE PROJECT 2019 (H2020 EU GA N 823886)
Projekte
- Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective / ProjektleiterIn / Projekt laufend
- REFRACT – Repeat protein Function, Refinement, Annotation and Classification of Topologies / ProjektleiterIn / Projekt laufend
- AI for colorectal cancer: towards the improved CMS classification and interpretability / ProjektleiterIn / Projekt abgeschlossen
- Die Exploration der Gen-Harmonisierung / Teammitglied / Projekt abgeschlossen
- Computational literature-based natural product drug discovery / Teammitglied / Projekt abgeschlossen
- The effect of programmed ribosomal frameshifting on codon usage bias / ProjektleiterIn / Projekt abgeschlossen
- Frequentist estimation of the evolutionary history of sequences with substitutions and indels / ProjektleiterIn / Projekt abgeschlossen
- Positive selection detection of genome from Ralstonia bacterium / ProjektleiterIn / Projekt abgeschlossen
- Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (Bio-SODA) / Teammitglied / Projekt abgeschlossen
- Exploring the silent fitness landscape / ProjektleiterIn / Projekt abgeschlossen
- Discovering evolutionary innovations by assessing variation and natural selection in protein tandem repeats / ProjektleiterIn / Projekt abgeschlossen
- Fast joint estimation of alignment and phylogeny from genomics sequences in a frequentist framework / ProjektleiterIn / Projekt abgeschlossen
Publikationen
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Verbiest, Max; Lundström, Oxana; Xia, Feifei; Baudis, Michael; Bilgin Sonay, Tugçe; Anisimova, Maria,
2024.
Short tandem repeat mutations regulate gene expression in colorectal cancer.
Scientific Reports.
14(1), S. 3331.
Verfügbar unter: https://doi.org/10.1038/s41598-024-53739-0
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Apsley, Abner T.; Domico, Emma R.; Verbiest, Max A.; Brogan, Carly A.; Buck, Evan R.; Burich, Andrew J.; Cardone, Kathleen M.; Stone, Wesley J.; Anisimova, Maria; Vandenbergh, David J.,
2023.
A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3).
Life Science Alliance.
6(4), S. e202201677.
Verfügbar unter: https://doi.org/10.26508/lsa.202201677
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Verbiest, Max; Maksimov, Mikhail; Jin, Ye; Anisimova, Maria; Gymrek, Melissa; Bilgin Sonay, Tugce,
2022.
Journal of Evolutionary Biology.
36(2), S. 321-336.
Verfügbar unter: https://doi.org/10.1111/jeb.14106
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Jowkar, Gholamhossein; Pecerska, Julija; Maiolo, Massimo; Gil, Manuel; Anisimova, Maria,
2022.
Systematic Biology.
72(2), S. 307-318.
Verfügbar unter: https://doi.org/10.1093/sysbio/syac050
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Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt,
2022.
Distributed and Parallel Databases.
40(2), S. 409-440.
Verfügbar unter: https://doi.org/10.1007/s10619-022-07414-w
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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
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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
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Nguyen, Huu-Giao; Lundström, Oxana; Blank, Annika; Dawson, Heather; Lugli, Alessandro; Anisimova, Maria; Zlobec, Inti,
2021.
Modern Pathology.
35, S. 240-248.
Verfügbar unter: https://doi.org/10.1038/s41379-021-00894-8
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Delucchi, Matteo; Näf, Paulina; Bliven, Spencer; Anisimova, Maria,
2021.
Frontiers in Bioinformatics.
1(691865).
Verfügbar unter: https://doi.org/10.3389/fbinf.2021.691865
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Verbiest, Max; Delucchi, Matteo; Bilgin Sonay, Tugce; Anisimova, Maria,
2021.
Frontiers in Bioinformatics.
1(685844).
Verfügbar unter: https://doi.org/10.3389/fbinf.2021.685844
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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
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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
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Sidorova, Julia; Anisimova, Maria,
2020.
Impact of diabetes mellitus on voice : a methodological commentary.
The Journal of Voice.
36(2), S. 294.E1-294.E12.
Verfügbar unter: https://doi.org/10.1016/j.jvoice.2020.05.015
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Delucchi, Matteo; Schaper, Elke; Sachenkova, Oxana; Elofsson, Arne; Anisimova, Maria,
2020.
A new census of protein tandem repeats and their relationship with intrinsic disorder.
Genes.
11(4), S. 407.
Verfügbar unter: https://doi.org/10.3390/genes11040407
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Silov, Serhii; Zaburannyi, Nestor; Anisimova, Maria; Ostash, Bohdan,
2020.
The use of the rare TTA codon in Streptomyces genes : significance of the codon context?.
Indian Journal of Microbiology.
61(1), S. 24-30.
Verfügbar unter: https://doi.org/10.1007/s12088-020-00902-6
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Tørresen, Ole K; Star, Bastiaan; Mier, Pablo; Andrade-Navarro, Miguel A; Bateman, Alex; Jarnot, Patryk; Gruca, Aleksandra; Grynberg, Marcin; Kajava, Andrey V; Promponas, Vasilis J; Anisimova, Maria; Jakobsen, Kjetill S; Linke, Dirk,
2019.
Nucleic Acids Research.
47(21), S. 10994-11006.
Verfügbar unter: https://doi.org/10.1093/nar/gkz841
-
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
-
Garcia, Victor; Zoller, Stefan; Anisimova, Maria,
2018.
Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices.
G3 - Genes, Genomes, Genetics.
8(10), S. 3173-3183.
Verfügbar unter: https://doi.org/10.1534/g3.118.200185
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Mattle-Greminger, Maja P.; Bilgin Sonay, Tugce; Nater, Alexander; Pybus, Marc; Desai, Tariq; de Valles, Guillem; Casals, Ferran; Scally, Aylwyn; Bertranpetit, Jaume; Marques-Bonet, Tomas; van Schaik, Carel P.; Anisimova, Maria; Krützen, Michael,
2018.
Genomes reveal marked differences in the adaptive evolution between orangutan species.
Genome Biology.
19(193).
Verfügbar unter: https://doi.org/10.1186/s13059-018-1562-6
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Rabyk, Mariia; Yushchuk, Oleksandr; Rokytskyy, Ihor; Anisimova, Maria; Ostash, Bohdan,
2018.
Journal of Molecular Evolution.
86(3-4), S. 204-215.
Verfügbar unter: https://doi.org/10.1007/s00239-018-9834-z
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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
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Nater, Alexander; Mattle-Greminger, Maja P.; Nurcahyo, Anton; Nowak, Matthew G.; de Manuel, Marc; Desai, Tariq; Groves, Colin; Pybus, Marc; Sonay, Tugce Bilgin; Roos, Christian; Lameira, Adriano R.; Wich, Serge A.; Askew, James; Davila-Ross, Marina; Fredriksson, Gabriella; de Valles, Guillem; Casals, Ferran; Prado-Martinez, Javier; Goossens, Benoit; Verschoor, Ernst J.; Warren, Kristin S.; Singleton, Ian; Marques, David A.; Pamungkas, Joko; Perwitasari-Farajallah, Dyah; Rianti, Puji; Tuuga, Augustine; Gut, Ivo G.; Gut, Marta; Orozco-terWengel, Pablo; van Schaik, Carel P.; Bertranpetit, Jaume; Anisimova, Maria; Scally, Aylwyn; Marques-Bonet, Tomas; Meijaard, Erik; Krützen, Michael,
2017.
Morphometric, behavioral, and genomic evidence for a new orangutan species.
Current Biology.
27(22), S. 3487-3498.e10.
Verfügbar unter: https://doi.org/10.1016/j.cub.2017.09.047
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Balakirev, Evgeniy S.; Anisimova, Maria; Pavlyuchkov, Vladimir A.; Ayala, Francisco J.,
2016.
DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).
BMC Genetics.
17, S. 66-82.
Verfügbar unter: https://doi.org/10.1186/s12863-016-0374-5
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Wang, Keke; Remigi, Philippe; Anisimova, Maria; Lonjon, Fabien; Kars, Ilona; Kajava, Andrey; Li, Chien-Hui; Cheng, Chiu-Ping; Vailleau, Fabienne; Genin, Stéphane; Peeters, Nemo,
2016.
Molecular Plant Pathology.
17(4), S. 553-564.
Verfügbar unter: https://doi.org/10.1111/mpp.12302
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Anisimova, Maria,
2015.
BMC Evolutionary Biology.
15, S. 76-85.
Verfügbar unter: https://doi.org/10.1186/s12862-015-0352-y
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Zoller, Stefan; Boskova, Veronika; Anisimova, Maria,
2015.
Maximum-likelihood tree estimation using codon substitution models with multiple partitions.
Molecular Biology and Evolution.
32(8), S. 2208-2216.
Verfügbar unter: https://doi.org/10.1093/molbev/msv097
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Anisimova, Maria; Pečerska, Jūlija; Schaper, Elke,
2015.
Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.
Frontiers in Bioengineering and Biotechnology.
3(31).
Verfügbar unter: https://doi.org/10.3389/fbioe.2015.00031
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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), S. D27-D37.
Verfügbar unter: https://doi.org/10.1093/nar/gkv1310
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Schaper, Elke; Korsunsky, Alexander; Pečerska, Jūlija; Messina, Antonio; Murri, Riccardo; Stockinger, Heinz; Zoller, Stefan; Xenarios, Ioannis; Anisimova, Maria,
2015.
TRAL : tandem repeat annotation library.
Bioinformatics.
31(18), S. 3051-3053.
Verfügbar unter: https://doi.org/10.1093/bioinformatics/btv306
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Mirsky, Alexander; Anisimova, Maria; Kazandjian, Linda,
2014.
Molecular Biology and Evolution.
32(3), S. 806-819.
Verfügbar unter: https://doi.org/10.1093/molbev/msu340
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Schaper, Elke; Gascuel, Olivier; Anisimova, Maria,
2014.
Deep conservation of human protein tandem repeats within the eukaryotes.
Molecular Biology and Evolution.
31(5), S. 1132-1148.
Verfügbar unter: https://doi.org/10.1093/molbev/msu062
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Schaper, Elke; Anisimova, Maria,
2014.
The evolution and function of protein tandem repeats in plants.
New Phytologist.
206(1), S. 397-410.
Verfügbar unter: https://doi.org/10.1111/nph.13184
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Dimitrieva, Slavica; Anisimova, Maria,
2014.
PLOS ONE.
9(6/e95034).
Verfügbar unter: https://doi.org/10.1371/journal.pone.0095034
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Anisimova, Maria, Hrsg.,
2019.
Evolutionary genomics : statistical and computational methods.
Second Edition.
New York:
Humana.
Methods in Molecular Biology.
ISBN 978-1-4939-9073-3.
Verfügbar unter: https://doi.org/10.1007/978-1-4939-9074-0
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Ostash, Bohdan; Anisimova, Maria,
2020.
Visualizing codon usage within and across genomes : concepts and tools
.
In:
Srinivasa, K. G.; Siddesh, G. M.; Manisekhar, S. R., Hrsg.,
Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications.
Singapore:
Springer.
S. 213-288.
Algorithms for Intelligent Systems.
Verfügbar unter: https://doi.org/10.1007/978-981-15-2445-5_13
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Kosiol, Carolin; Anisimova, Maria,
2019.
.
In:
Anisimova, Maria, Hrsg.,
Evolutionary genomics : statistical and computational methods.
Humana.
S. 373-397.
Methods in Molecular Biology.
Verfügbar unter: https://doi.org/10.1007/978-1-4939-9074-0_12
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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
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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
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Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt,
2021.
Bio-SODA : enabling natural language question answering over knowledge graphs without training data [Paper].
In:
Proceedings of the 33rd SSDBM.
International Conference on Scientific and Statistical Database Management (SSDBM), Online, 6-7 July 2021.
Association for Computing Machinery.
S. 61-72.
Verfügbar unter: https://doi.org/10.1145/3468791.3469119
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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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Garcia, Victor; Zoller, Stefan; Anisimova, Maria,
2018.
Programmed ribosomal frameshifting and codon usage bias [Poster].
In:
Hirsch, Sven, Hrsg.,
Life in Numbers 4.0.
Life in Numbers 4, Wädenswil, 4 October 2018.
ZHAW Zürcher Hochschule für Angewandte Wissenschaften.
Verfügbar unter: https://doi.org/10.21256/zhaw-4023
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Bliven, Spencer; Anisimova, Maria,
2018.
Phylogentics of tandem repeats with circular HMMs : a case study on Armadillo Repeat Proteins [Poster].
In:
SIB-Days, Biel/Bienne, 26-27 June 2018.
ZHAW Zürcher Hochschule für Angewandte Wissenschaften.
Verfügbar unter: https://doi.org/10.21256/zhaw-3861
-
Garcia, Victor; Zoller, Stefan; Anisimova, Maria,
2018.
Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices [Poster].
In:
Symposium on Quantitative Network Biology, Kandersteg, 19-20 November 2018.
-
Bliven, Spencer; Anisimova, Maria,
2017.
Phylogenetics of tandem repeats with circular HMMs : a case study on Armadillo Repeat Proteins [Poster].
In:
NGP-Net 2017, Symposium on Non-globular Proteins, Kosice, Slovakia, August 2017.
ZHAW Zürcher Hochschule für Angewandte Wissenschaften.
S. 1.
Verfügbar unter: https://doi.org/10.21256/zhaw-4269
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Anisimova, Maria; Gatti, Lorenzo,
2017.
Phylogenetics reveals competition of human flu subtypes.
TRANSFER.
2017(1), S. 12.
Verfügbar unter: https://doi.org/10.21256/zhaw-4270
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Anisimova, Maria,
2016.
Verfügbar unter: https://www.youtube.com/watch?v=np9xXnxrvoc
-
Anisimova, Maria,
2014.
Joint alignmnet and phylogeny for large genomics data.
TRANSFER.
2014(3).
Verfügbar unter: https://doi.org/10.21256/zhaw-3887
-
Rech, Gabriel E.; Sanz-Martín, José M.; Anisimova, Maria; Sukno, Serenella A.; Thon, Michael R.,
2014.
Genome Biology and Evolution.
6(9), S. 2368-2379.
Verfügbar unter: https://doi.org/10.1093/gbe/evu192
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Anisimova, Maria; Dessimoz, Christophe, Hrsg.,
2014.
Proceedings of GNOME 2014 : Festschrift for Gaston Gonnet.
GNOME 2014 Symposium in Honour of Gaston Gonnet's Retirement, Zurich, Switzerland, 4 July 2014.
Zürich:
PeerJ.
.
Verfügbar unter: https://peerj.com/collections/7-gastongonnetfestchrift/
-
Anisimova, Maria,
2017.
Detecting selection signature in genomics sequences.
In:
CBID Computational Biology for Infectious Diseases Summer School, Quy Nhon, Vietnam, 17-24 September 2017.
ICISE.
-
Anisimova, Maria,
2017.
Phylogenetic methods for detecting natural selection in genomic sequences.
In:
Scientific and Technological Developments of Research and Monitoring of Marine Biological Resources, Vladivostok, Russia, 22-24 May 2017.
-
Osterhaus, Albert D M E; Schutten, Martin; Van der Vries, Erhard; Zhang, Jitao David; Boucher, Charles A; Anisimova, Maria; Gatti, Lorenzo,
2016.
In:
ZHAW-Forum «Health & Life Sciences», Wädenswil, 2016.
-
Anisimova, Maria,
2016.
Evolution from mathematician to bioinformatician by natural selection.
In:
POST-DOC-DOC 2.0, Life Sciences, Schloss Au, Wädenswil, 2016.
-
Anisimova, Maria,
2015.
Computational methods for detecting and analyzing tandem repeats.
In:
Non-globular proteins - from sequence to structure, function and application in molecular physiopathology, NGP-NET Symposium, Portol, Spain, 6-9 October 2015.
-
Anisimova, Maria,
2015.
Disentangling tandem repeats, their evolution and roles in genomic sequences.
In:
EES Seminar Series LMU, München, Deutschland, 2015.
-
Anisimova, Maria,
2015.
Next generation comparative phylogenomics.
In:
StarOmics Symposium, Geneva, 2015.
-
Anisimova, Maria,
2014.
In:
Lycée de la Planta, Sion, 2014.
-
Anisimova, Maria,
2014.
Visualisation of multiple sequence alignment and phylogeny.
In:
2nd EMBO Visualizing Biological Data (VIZBI 2014), Heidelberg, 5-7 March 2014.
Verfügbar unter: https://www.vizbi.org/2014/Speakers/