Prof. Dr. Maria Anisimova

ZHAW School of Life Sciences and Facility Management
FS Bioinformatics
Schloss 1
8820 Wädenswil

+41 (0) 58 934 58 82
maria.anisimova@zhaw.ch

Projects

Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective / Project leader / Project ongoing
REFRACT – Repeat protein Function, Refinement, Annotation and Classification of Topologies / Project leader / Project ongoing
AI for colorectal cancer: towards the improved CMS classification and interpretability / Project leader / Project completed
Die Exploration der Gen-Harmonisierung / Team member / Project completed
Computational literature-based natural product drug discovery / Team member / Project completed
The effect of programmed ribosomal frameshifting on codon usage bias / Project leader / Project completed
Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Project leader / Project completed
Positive selection detection of genome from Ralstonia bacterium / Project leader / 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
Exploring the silent fitness landscape / Project leader / Project completed
Discovering evolutionary innovations by assessing variation and natural selection in protein tandem repeats / Project leader / Project completed
Fast joint estimation of alignment and phylogeny from genomics sequences in a frequentist framework / Project leader / Project completed

Publications

Articles in scientific journal, peer-reviewed

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), pp. e202201677.

Available from: https://doi.org/10.26508/lsa.202201677
Verbiest, Max; Maksimov, Mikhail; Jin, Ye; Anisimova, Maria; Gymrek, Melissa; Bilgin Sonay, Tugce,

2022.

Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.

Journal of Evolutionary Biology.

36(2), pp. 321-336.

Available from: https://doi.org/10.1111/jeb.14106
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
Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt,

2022.

Bio-SODA UX : enabling natural language question answering over knowledge graphs with user disambiguation.

Distributed and Parallel Databases.

40(2), pp. 409-440.

Available from: https://doi.org/10.1007/s10619-022-07414-w
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
Nguyen, Huu-Giao; Lundström, Oxana; Blank, Annika; Dawson, Heather; Lugli, Alessandro; Anisimova, Maria; Zlobec, Inti,

2021.

Image-based assessment of extracellular mucin-to-tumor area predicts consensus molecular subtypes (CMS) in colorectal cancer.

Modern Pathology.

35, pp. 240-248.

Available from: https://doi.org/10.1038/s41379-021-00894-8
Delucchi, Matteo; Näf, Paulina; Bliven, Spencer; Anisimova, Maria,

2021.

TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner.

Frontiers in Bioinformatics.

1(691865).

Available from: https://doi.org/10.3389/fbinf.2021.691865
Verbiest, Max; Delucchi, Matteo; Bilgin Sonay, Tugce; Anisimova, Maria,

2021.

Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer.

Frontiers in Bioinformatics.

1(685844).

Available from: https://doi.org/10.3389/fbinf.2021.685844
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
Sidorova, Julia; Anisimova, Maria,

2020.

Impact of diabetes mellitus on voice : a methodological commentary.

The Journal of Voice.

36(2), pp. 294.E1-294.E12.

Available from: https://doi.org/10.1016/j.jvoice.2020.05.015
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), pp. 407.

Available from: https://doi.org/10.3390/genes11040407
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), pp. 24-30.

Available from: https://doi.org/10.1007/s12088-020-00902-6
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.

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

Nucleic Acids Research.

47(21), pp. 10994-11006.

Available from: 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).

Available from: 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), pp. 3173-3183.

Available from: https://doi.org/10.1534/g3.118.200185
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).

Available from: https://doi.org/10.1186/s13059-018-1562-6
Rabyk, Mariia; Yushchuk, Oleksandr; Rokytskyy, Ihor; Anisimova, Maria; Ostash, Bohdan,

2018.

Genomic insights into evolution of AdpA family master regulators of morphological differentiation and secondary metabolism in streptomyces.

Journal of Molecular Evolution.

86(3-4), pp. 204-215.

Available from: https://doi.org/10.1007/s00239-018-9834-z
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
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), pp. 3487-3498.e10.

Available from: https://doi.org/10.1016/j.cub.2017.09.047
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, pp. 66-82.

Available from: https://doi.org/10.1186/s12863-016-0374-5
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.

Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum.

Molecular Plant Pathology.

17(4), pp. 553-564.

Available from: https://doi.org/10.1111/mpp.12302
Anisimova, Maria,

2015.

Darwin and Fisher meet at biotech : on the potential of computational molecular evolution in industry.

BMC Evolutionary Biology.

15, pp. 76-85.

Available from: https://doi.org/10.1186/s12862-015-0352-y
Zoller, Stefan; Boskova, Veronika; Anisimova, Maria,

2015.

Maximum-likelihood tree estimation using codon substitution models with multiple partitions.

Molecular Biology and Evolution.

32(8), pp. 2208-2216.

Available from: https://doi.org/10.1093/molbev/msv097
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).

Available from: https://doi.org/10.3389/fbioe.2015.00031
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
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), pp. 3051-3053.

Available from: https://doi.org/10.1093/bioinformatics/btv306
Mirsky, Alexander; Anisimova, Maria; Kazandjian, Linda,

2014.

Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences.

Molecular Biology and Evolution.

32(3), pp. 806-819.

Available from: https://doi.org/10.1093/molbev/msu340
Schaper, Elke; Gascuel, Olivier; Anisimova, Maria,

2014.

Deep conservation of human protein tandem repeats within the eukaryotes.

Molecular Biology and Evolution.

31(5), pp. 1132-1148.

Available from: https://doi.org/10.1093/molbev/msu062
Schaper, Elke; Anisimova, Maria,

2014.

The evolution and function of protein tandem repeats in plants.

New Phytologist.

206(1), pp. 397-410.

Available from: https://doi.org/10.1111/nph.13184
Dimitrieva, Slavica; Anisimova, Maria,

2014.

Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.

PLOS ONE.

9(6/e95034).

Available from: https://doi.org/10.1371/journal.pone.0095034

Books and monographs, peer-reviewed

Anisimova, Maria, ed.,

2019.

Evolutionary genomics : statistical and computational methods.

Second Edition.

New York:

Humana.

Methods in Molecular Biology.

ISBN 978-1-4939-9073-3.

Available from: https://doi.org/10.1007/978-1-4939-9074-0

Book parts, peer-reviewed

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., eds.,

Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications.

Singapore:

Springer.

pp. 213-288.

Algorithms for Intelligent Systems.

Available from: https://doi.org/10.1007/978-981-15-2445-5_13
Kosiol, Carolin; Anisimova, Maria,

2019.

Selection acting on genomes

.

In:

Anisimova, Maria, ed.,

Evolutionary genomics : statistical and computational methods.

Humana.

pp. 373-397.

Methods in Molecular Biology.

Available from: https://doi.org/10.1007/978-1-4939-9074-0_12
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

Conference contributions, peer-reviewed

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
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.

pp. 61-72.

Available from: https://doi.org/10.1145/3468791.3469119
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

Other publications

Garcia, Victor; Zoller, Stefan; Anisimova, Maria,

2018.

Programmed ribosomal frameshifting and codon usage bias [poster].

In:

Hirsch, Sven, ed.,

Life in Numbers 4.0.

Life in Numbers 4, Wädenswil, 4 October 2018.

ZHAW Zürcher Hochschule für Angewandte Wissenschaften.

Available from: https://doi.org/10.21256/zhaw-4023
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.

Available from: 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.

pp. 1.

Available from: https://doi.org/10.21256/zhaw-4269
Anisimova, Maria; Gatti, Lorenzo,

2017.

Phylogenetics reveals competition of human flu subtypes.

TRANSFER.

2017(1), pp. 12.

Available from: https://doi.org/10.21256/zhaw-4270
Anisimova, Maria,

2016.

Disentangling tandem repeats and their evolutionary histories usinf statistical prediction, Virtual Computational Biology Seminar Series, Lausanne SIB.

Available from: https://www.youtube.com/watch?v=np9xXnxrvoc
Anisimova, Maria,

2014.

Joint alignmnet and phylogeny for large genomics data.

TRANSFER.

2014(3).

Available from: https://doi.org/10.21256/zhaw-3887
Rech, Gabriel E.; Sanz-Martín, José M.; Anisimova, Maria; Sukno, Serenella A.; Thon, Michael R.,

2014.

Natural selection at coding and non-coding DNA mainly affects pathogenicity-related genes in the hemibiotrophic fungus Colletotrichum graminicola.

Genome Biology and Evolution.

6(9), pp. 2368-2379.

Available from: https://doi.org/10.1093/gbe/evu192
Anisimova, Maria; Dessimoz, Christophe, eds.,

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.

.

Available from: https://peerj.com/collections/7-gastongonnetfestchrift/

Oral conference contributions and abstracts

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.

As a stone thrown in a still pond : predicting human influenza epidemiological dynamics after 2009 A/pH1N1 pandemic explosion.

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.

Bioinformatique et génomique.

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.

Available from: https://www.vizbi.org/2014/Speakers/

go back