Prof. Dr. Maria Anisimova

Projects

• Harnessing indel history statistics for molecular biomarker detection in viral genomes / Project leader / ongoing
• Inferring the molecular evolutionary history with multiple-character indels: from theory to practice / Project leader / ongoing
• Novel Markov chain Monte Carlo algorithms for Bayesian inference / Project leader / completed
• AI for colorectal cancer: towards the improved CMS classification and interpretability / Project leader / completed
• Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective / Project leader / completed
• Computational literature-based natural product drug discovery / Team member / completed
• Repeat protein Function, Refinement, Annotation and Classification of Topologies / Project leader / completed
• The effect of programmed ribosomal frameshifting on codon usage bias / Project leader / completed
• Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Project leader / completed
• Positive selection detection of genome from Ralstonia bacterium / Project leader / completed
• Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data / Team member / completed
• Exploring the silent fitness landscape / Project leader / completed
• Discovering evolutionary innovations by assessing variation and natural selection in protein tandem repeats / Project leader / completed
• Fast joint estimation of alignment and phylogeny from genomics sequences in a frequentist framework / Project leader / completed

Publications

Articles in scientific journal, peer-reviewed

• Kondrateva, O., Bilgin Sonay, T., Zlobec, I., & Anisimova, M. (2026). Tumor mutational burden predicts neoantigen profiles and immunotherapy response in microsatellite stable tumors across different cancer types. Frontiers in Immunology, 16(1582464). https://doi.org/10.3389/fimmu.2025.1582464
• Verbiest, M. A., Grassi, E., Bertotti, A., & Anisimova, M. (2025). Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms. Communications Biology, 8(1437). https://doi.org/10.1038/s42003-025-08837-8
• Seppey, M., Iglhaut, C., Gil, M., & Anisimova, M. (2025). Impact of phylogenetic method choice on Iindel analyses in HIV-1 subtype B. Genome Biology and Evolution, 17(6), evaf119. https://doi.org/10.1093/gbe/evaf119
• Xia, F., Verbiest, M. A., Lundström, O., Bilgin Sonay, T., Baudis, M., & Anisimova, M. (2025). Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms. Briefings in Bioinformatics, 26(3), bbaf219. https://doi.org/10.1093/bib/bbaf219
• Redelings, B. D., Holmes, I., Lunter, G., Pupko, T., & Anisimova, M. (2024). Insertions and deletions : computational methods, evolutionary dynamics, and biological applications. Molecular Biology and Evolution, 41(9), msae177. https://doi.org/10.1093/molbev/msae177
• Verbiest, M., Lundström, O., Xia, F., Baudis, M., Bilgin Sonay, T., & Anisimova, M. (2024). Short tandem repeat mutations regulate gene expression in colorectal cancer. Scientific Reports, 14(1), 3331. https://doi.org/10.1038/s41598-024-53739-0
• Apsley, A. T., Domico, E. R., Verbiest, M. A., Brogan, C. A., Buck, E. R., Burich, A. J., Cardone, K. M., Stone, W. J., Anisimova, M., & Vandenbergh, D. J. (2023). A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Science Alliance, 6(4), e202201677. https://doi.org/10.26508/lsa.202201677
• Verbiest, M., Maksimov, M., Jin, Y., Anisimova, M., Gymrek, M., & Bilgin Sonay, T. (2022). Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. Journal of Evolutionary Biology, 36(2), 321–336. https://doi.org/10.1111/jeb.14106
• Sima, A. C., Mendes de Farias, T., Anisimova, M., Dessimoz, C., Robinson-Rechavi, M., Zbinden, E., & Stockinger, K. (2022). Bio-SODA UX : enabling natural language question answering over knowledge graphs with user disambiguation. Distributed and Parallel Databases, 40(2), 409–440. https://doi.org/10.1007/s10619-022-07414-w
• Jowkar, G., Pecerska, J., Maiolo, M., Gil, M., & Anisimova, M. (2022). ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process. Systematic Biology, 72(2), 307–318. https://doi.org/10.1093/sysbio/syac050
• Lardos, A., Aghaebrahimian, A., Koroleva, A., Sidorova, J., Wolfram, E., Anisimova, M., & Gil, M. (2022). Computational literature-based discovery for natural products research : current state and future prospects. Frontiers in Bioinformatics, 2(827207). https://doi.org/10.3389/fbinf.2022.827207
• Maiolo, M., Gatti, L., Frei, D., Leidi, T., Gil, M., & Anisimova, M. (2021). ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics, 22(1), 518. https://doi.org/10.1186/s12859-021-04442-8
• Nguyen, H.-G., Lundström, O., Blank, A., Dawson, H., Lugli, A., Anisimova, M., & Zlobec, I. (2021). Image-based assessment of extracellular mucin-to-tumor area predicts consensus molecular subtypes (CMS) in colorectal cancer. Modern Pathology, 35, 240–248. https://doi.org/10.1038/s41379-021-00894-8
• Delucchi, M., Näf, P., Bliven, S., & Anisimova, M. (2021). TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner. Frontiers in Bioinformatics, 1(691865). https://doi.org/10.3389/fbinf.2021.691865
• Verbiest, M., Delucchi, M., Bilgin Sonay, T., & Anisimova, M. (2021). Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer. Frontiers in Bioinformatics, 1(685844). https://doi.org/10.3389/fbinf.2021.685844
• Liang, S., Stockinger, K., de Farias, T. M., Anisimova, M., & Gil, M. (2021). Querying knowledge graphs in natural language. Journal of Big Data, 8(3). https://doi.org/10.1186/s40537-020-00383-w
• Silov, S., Zaburannyi, N., Anisimova, M., & Ostash, B. (2020). The use of the rare TTA codon in Streptomyces genes : significance of the codon context? Indian Journal of Microbiology, 61(1), 24–30. https://doi.org/10.1007/s12088-020-00902-6
• Maiolo, M., Ulzega, S., Gil, M., & Anisimova, M. (2020). Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform. NAR Genomics and Bioinformatics, 2(4), lqaa092. https://doi.org/10.1093/nargab/lqaa092
• Sidorova, J., & Anisimova, M. (2020). Impact of diabetes mellitus on voice : a methodological commentary. The Journal of Voice, 36(2), 294. https://doi.org/10.1016/j.jvoice.2020.05.015
• Delucchi, M., Schaper, E., Sachenkova, O., Elofsson, A., & Anisimova, M. (2020). A new census of protein tandem repeats and their relationship with intrinsic disorder. Genes, 11(4), 407. https://doi.org/10.3390/genes11040407
• Sima, A.-C., Mendes de Farias, T., Zbinden, E., Anisimova, M., Gil, M., Stockinger, H., Stockinger, K., Robinson-Rechavi, M., & Dessimoz, C. (2019). Enabling semantic queries across federated bioinformatics databases. Database: The Journal of Biological Databases and Curation, 2019(baz106). https://doi.org/10.1093/database/baz106
• Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., Anisimova, M., Jakobsen, K. S., & Linke, D. (2019). Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Research, 47(21), 10994–11006. https://doi.org/10.1093/nar/gkz841
• Maiolo, M., Zhang, X., Gil, M., & Anisimova, M. (2018). Progressive multiple sequence alignment with indel evolution. BMC Bioinformatics, 19(331). https://doi.org/10.1186/s12859-018-2357-1
• Mattle-Greminger, M. P., Bilgin Sonay, T., Nater, A., Pybus, M., Desai, T., de Valles, G., Casals, F., Scally, A., Bertranpetit, J., Marques-Bonet, T., van Schaik, C. P., Anisimova, M., & Krützen, M. (2018). Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biology, 19(193). https://doi.org/10.1186/s13059-018-1562-6
• Rabyk, M., Yushchuk, O., Rokytskyy, I., Anisimova, M., & Ostash, B. (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), 204–215. https://doi.org/10.1007/s00239-018-9834-z
• Garcia, V., Zoller, S., & Anisimova, M. (2018). Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices. G3 - Genes, Genomes, Genetics, 8(10), 3173–3183. https://doi.org/10.1534/g3.118.200185
• Nater, A., Mattle-Greminger, M. P., Nurcahyo, A., Nowak, M. G., de Manuel, M., Desai, T., Groves, C., Pybus, M., Sonay, T. B., Roos, C., Lameira, A. R., Wich, S. A., Askew, J., Davila-Ross, M., Fredriksson, G., de Valles, G., Casals, F., Prado-Martinez, J., Goossens, B., et al. (2017). Morphometric, behavioral, and genomic evidence for a new orangutan species. Current Biology, 27(22), 3487–3498. https://doi.org/10.1016/j.cub.2017.09.047
• Wang, K., Remigi, P., Anisimova, M., Lonjon, F., Kars, I., Kajava, A., Li, C.-H., Cheng, C.-P., Vailleau, F., Genin, S., & Peeters, N. (2016). Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum. Molecular Plant Pathology, 17(4), 553–564. https://doi.org/10.1111/mpp.12302
• Balakirev, E. S., Anisimova, M., Pavlyuchkov, V. A., & Ayala, F. J. (2016). DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea). BMC Genetics, 17, 66–82. https://doi.org/10.1186/s12863-016-0374-5
• Anisimova, M. (2015). Darwin and Fisher meet at biotech : on the potential of computational molecular evolution in industry. BMC Evolutionary Biology, 15, 76–85. https://doi.org/10.1186/s12862-015-0352-y
• Zoller, S., Boskova, V., & Anisimova, M. (2015). Maximum-likelihood tree estimation using codon substitution models with multiple partitions. Molecular Biology and Evolution, 32(8), 2208–2216. https://doi.org/10.1093/molbev/msv097
• Anisimova, M., Gatti, L., Gil, M., & Maiolo, M. (2015). The SIB Swiss Institute of Bioinformatics’ resources : focus on curated databases. Nucleic Acids Research, 44(D1), D27–D37. https://doi.org/10.1093/nar/gkv1310
• Schaper, E., Korsunsky, A., Pečerska, J., Messina, A., Murri, R., Stockinger, H., Zoller, S., Xenarios, I., & Anisimova, M. (2015). TRAL : tandem repeat annotation library. Bioinformatics, 31(18), 3051–3053. https://doi.org/10.1093/bioinformatics/btv306
• Anisimova, M., Pečerska, J., & Schaper, E. (2015). Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Frontiers in Bioengineering and Biotechnology, 3(31). https://doi.org/10.3389/fbioe.2015.00031
• Mirsky, A., Anisimova, M., & Kazandjian, L. (2014). Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences. Molecular Biology and Evolution, 32(3), 806–819. https://doi.org/10.1093/molbev/msu340
• Rech, G. E., Sanz-Martín, J. M., Anisimova, M., Sukno, S. A., & Thon, M. 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), 2368–2379. https://doi.org/10.1093/gbe/evu192
• Schaper, E., & Anisimova, M. (2014). The evolution and function of protein tandem repeats in plants. New Phytologist, 206(1), 397–410. https://doi.org/10.1111/nph.13184
• Schaper, E., Gascuel, O., & Anisimova, M. (2014). Deep conservation of human protein tandem repeats within the eukaryotes. Molecular Biology and Evolution, 31(5), 1132–1148. https://doi.org/10.1093/molbev/msu062
• Dimitrieva, S., & Anisimova, M. (2014). Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. Plos One, 9(6/e95034). https://doi.org/10.1371/journal.pone.0095034

Books, peer-reviewed

Anisimova, M. (2019). Evolutionary genomics : statistical and computational methods (Second Edition). Humana. https://doi.org/10.1007/978-1-4939-9074-0

Book chapters, peer-reviewed

• Ostash, B., & Anisimova, M. (2020). Visualizing codon usage within and across genomes : concepts and tools. In K. G. Srinivasa, G. M. Siddesh, & S. R. Manisekhar (Eds.), Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications (pp. 213–288). Springer. https://doi.org/10.1007/978-981-15-2445-5_13
• Kosiol, C., & Anisimova, M. (2019). Selection acting on genomes. In M. Anisimova (Ed.), Evolutionary genomics : statistical and computational methods (pp. 373–397). Humana. https://doi.org/10.1007/978-1-4939-9074-0_12
• Gil, M., & Anisimova, M. (2015). Methodologies for phylogenetic inference. In Encyclopedia of life sciences. Wiley. https://doi.org/10.1002/9780470015902.a0025545

Written conference contributions, peer-reviewed

• Aghaebrahimian, A., Anisimova, M., & Gil, M. (2022). Ontology-aware biomedical relation extraction [Conference paper]. In P. Sojka, A. Horák, I. Kopeček, & K. Pala (Eds.), Text, Speech, and Dialogue (pp. 160–171). Springer. https://doi.org/10.1007/978-3-031-16270-1_14
• Sima, A. C., Mendes de Farias, T., Anisimova, M., Dessimoz, C., Robinson-Rechavi, M., Zbinden, E., & Stockinger, K. (2021). Bio-SODA : enabling natural language question answering over knowledge graphs without training data [Conference paper]. Proceedings of the 33rd SSDBM, 61–72. https://doi.org/10.1145/3468791.3469119
• Koroleva, A., Anisimova, M., & Gil, M. (2020). Towards creating a new triple store for literature-based discovery [Conference paper]. In W. Lu & K. Q. Zhu (Eds.), Trends and Applications in Knowledge Discovery and Data Mining. PAKDD 2020 (pp. 41–50). Springer. https://doi.org/10.1007/978-3-030-60470-7_5

Other publications

• Garcia, V., Zoller, S., & Anisimova, M. (2018). Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices. Symposium on Quantitative Network Biology, Kandersteg, 19-20 November 2018.
• Garcia, V., Zoller, S., & Anisimova, M. (2018). Programmed ribosomal frameshifting and codon usage bias [Conference poster]. In S. Hirsch (Ed.), Life in Numbers 4.0. ZHAW Zürcher Hochschule für Angewandte Wissenschaften. https://doi.org/10.21256/zhaw-4023
• Bliven, S., & Anisimova, M. (2018, June 26). Phylogentics of tandem repeats with circular HMMs : a case study on Armadillo Repeat Proteins. SIB-Days, Biel/Bienne, 26-27 June 2018. https://doi.org/10.21256/zhaw-3861
• Anisimova, M., & Gatti, L. (2017). Phylogenetics reveals competition of human flu subtypes. Transfer, 2017(1), 12. https://doi.org/10.21256/zhaw-4270
• Bliven, S., & Anisimova, M. (2017). Phylogenetics of tandem repeats with circular HMMs : a case study on Armadillo Repeat Proteins [Conference poster]. NGP-Net 2017, Symposium on Non-Globular Proteins, Kosice, Slovakia, August 2017, 3, 1. https://doi.org/10.21256/zhaw-4269
• Anisimova, M. (2016). Disentangling tandem repeats and their evolutionary histories usinf statistical prediction, Virtual Computational Biology Seminar Series, Lausanne SIB. https://www.youtube.com/watch?v=np9xXnxrvoc
• Anisimova, M. (2014). Joint alignmnet and phylogeny for large genomics data. Transfer, 2014(3). https://doi.org/10.21256/zhaw-3887
• Proceedings of GNOME 2014 : Festschrift for Gaston Gonnet. (2014). In M. Anisimova & C. Dessimoz (Eds.), GNOME 2014 Symposium in Honour of Gaston Gonnet’s Retirement, Zurich, Switzerland, 4 July 2014. PeerJ. https://peerj.com/collections/7-gastongonnetfestchrift/

Oral conference contributions and abstracts

• Anisimova, M. (2017, September). Detecting selection signature in genomics sequences. CBID Computational Biology for Infectious Diseases Summer School, Quy Nhon, Vietnam, 17-24 September 2017.
• Anisimova, M. (2017, May). Phylogenetic methods for detecting natural selection in genomic sequences. Scientific and Technological Developments of Research and Monitoring of Marine Biological Resources, Vladivostok, Russia, 22-24 May 2017.
• Osterhaus, A. D. M. E., Schutten, M., Van der Vries, E., Zhang, J. D., Boucher, C. A., Anisimova, M., & Gatti, L. (2016). As a stone thrown in a still pond : predicting human influenza epidemiological dynamics after 2009 A/pH1N1 pandemic explosion. ZHAW-Forum «Health & Life Sciences», Wädenswil, 2016.
• Anisimova, M. (2016). Evolution from mathematician to bioinformatician by natural selection. POST-DOC-DOC 2.0, Life Sciences, Schloss Au, Wädenswil, 2016.
• Anisimova, M. (2015). Disentangling tandem repeats, their evolution and roles in genomic sequences. EES Seminar Series LMU, München, Deutschland, 2015.
• Anisimova, M. (2015). Next generation comparative phylogenomics. StarOmics Symposium, Geneva, 2015.
• Anisimova, M. (2015). Computational methods for detecting and analyzing tandem repeats. Non-Globular Proteins - from Sequence to Structure, Function and Application in Molecular Physiopathology, NGP-NET Symposium, Portol, Spain, 6-9 October 2015.
• Anisimova, M. (2014). Bioinformatique et génomique. Lycée de la Planta, Sion, 2014.
• Anisimova, M. (2014). Visualisation of multiple sequence alignment and phylogeny. 2nd EMBO Visualizing Biological Data (VIZBI 2014), Heidelberg, 5-7 March 2014. https://www.vizbi.org/2014/Speakers/

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