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. et al. (2026) ‘Tumor mutational burden predicts neoantigen profiles and immunotherapy response in microsatellite stable tumors across different cancer types’, Frontiers in Immunology, 16(1582464). doi: 10.3389/fimmu.2025.1582464.
• Verbiest, M. A. et al. (2025) ‘Genotyping short tandem repeats across copy number alterations, aneuploidies, and polyploid organisms’, Communications Biology, 8(1437). doi: 10.1038/s42003-025-08837-8.
• Seppey, M. et al. (2025) ‘Impact of phylogenetic method choice on Iindel analyses in HIV-1 subtype B’, Genome Biology and Evolution, 17(6), p. evaf119. doi: 10.1093/gbe/evaf119.
• Xia, F. et al. (2025) ‘Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms’, Briefings in Bioinformatics, 26(3), p. bbaf219. doi: 10.1093/bib/bbaf219.
• Jowkar, G. et al. (2024) ‘Single-character insertion–deletion model preserves long indels in ancestral sequence reconstruction’, BMC Bioinformatics, 25(370). doi: 10.1186/s12859-024-05986-1.
• Redelings, B. D. et al. (2024) ‘Insertions and deletions : computational methods, evolutionary dynamics, and biological applications’, Molecular Biology and Evolution, 41(9), p. msae177. doi: 10.1093/molbev/msae177.
• Verbiest, M. et al. (2024) ‘Short tandem repeat mutations regulate gene expression in colorectal cancer’, Scientific Reports, 14(1), p. 3331. doi: 10.1038/s41598-024-53739-0.
• Apsley, A. T. et al. (2023) ‘A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)’, Life Science Alliance, 6(4), p. e202201677. doi: 10.26508/lsa.202201677.
• Verbiest, M. et al. (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. doi: 10.1111/jeb.14106.
• Sima, A. C. et al. (2022) ‘Bio-SODA UX : enabling natural language question answering over knowledge graphs with user disambiguation’, Distributed and Parallel Databases, 40(2), pp. 409–440. doi: 10.1007/s10619-022-07414-w.
• Jowkar, G. et al. (2022) ‘ARPIP : ancestral sequence reconstruction with insertions and deletions under the poisson indel process’, Systematic Biology, 72(2), pp. 307–318. doi: 10.1093/sysbio/syac050.
• Lardos, A. et al. (2022) ‘Computational literature-based discovery for natural products research : current state and future prospects’, Frontiers in Bioinformatics, 2(827207). doi: 10.3389/fbinf.2022.827207.
• Maiolo, M. et al. (2021) ‘ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process’, BMC Bioinformatics, 22(1), p. 518. doi: 10.1186/s12859-021-04442-8.
• Nguyen, H.-G. et al. (2021) ‘Image-based assessment of extracellular mucin-to-tumor area predicts consensus molecular subtypes (CMS) in colorectal cancer’, Modern Pathology, 35, pp. 240–248. doi: 10.1038/s41379-021-00894-8.
• Delucchi, M. et al. (2021) ‘TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner’, Frontiers in Bioinformatics, 1(691865). doi: 10.3389/fbinf.2021.691865.
• Verbiest, M. et al. (2021) ‘Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer’, Frontiers in Bioinformatics, 1(685844). doi: 10.3389/fbinf.2021.685844.
• Liang, S. et al. (2021) ‘Querying knowledge graphs in natural language’, Journal of Big Data, 8(3). doi: 10.1186/s40537-020-00383-w.
• Silov, S. et al. (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. doi: 10.1007/s12088-020-00902-6.
• Maiolo, M. et al. (2020) ‘Accelerating phylogeny-aware alignment with indel evolution using short time Fourier transform’, NAR Genomics and Bioinformatics, 2(4), p. lqaa092. doi: 10.1093/nargab/lqaa092.
• Sidorova, J. and Anisimova, M. (2020) ‘Impact of diabetes mellitus on voice : a methodological commentary’, The Journal of Voice, 36(2), p. 294.E1–294.E12. doi: 10.1016/j.jvoice.2020.05.015.
• Delucchi, M. et al. (2020) ‘A new census of protein tandem repeats and their relationship with intrinsic disorder’, Genes, 11(4), p. 407. doi: 10.3390/genes11040407.
• Sima, A.-C. et al. (2019) ‘Enabling semantic queries across federated bioinformatics databases’, Database: The Journal of Biological Databases and Curation, 2019(baz106). doi: 10.1093/database/baz106.
• Tørresen, O. K. et al. (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. doi: 10.1093/nar/gkz841.
• Rabyk, M. et al. (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. doi: 10.1007/s00239-018-9834-z.
• Mattle-Greminger, M. P. et al. (2018) ‘Genomes reveal marked differences in the adaptive evolution between orangutan species’, Genome Biology, 19(193). doi: 10.1186/s13059-018-1562-6.
• Maiolo, M. et al. (2018) ‘Progressive multiple sequence alignment with indel evolution’, BMC Bioinformatics, 19(331). doi: 10.1186/s12859-018-2357-1.
• Garcia, V., Zoller, S. and Anisimova, M. (2018) ‘Accounting for programmed ribosomal frameshifting in the computation of codon usage bias indices’, G3 - Genes, Genomes, Genetics, 8(10), pp. 3173–3183. doi: 10.1534/g3.118.200185.
• Nater, A. et al. (2017) ‘Morphometric, behavioral, and genomic evidence for a new orangutan species’, Current Biology, 27(22), pp. 3487–3498.e10. doi: 10.1016/j.cub.2017.09.047.
• Wang, K. et al. (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. doi: 10.1111/mpp.12302.
• Balakirev, E. S. et al. (2016) ‘DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea)’, BMC Genetics, 17, pp. 66–82. doi: 10.1186/s12863-016-0374-5.
• Schaper, E. et al. (2015) ‘TRAL : tandem repeat annotation library’, Bioinformatics, 31(18), pp. 3051–3053. doi: 10.1093/bioinformatics/btv306.
• Anisimova, M., Pečerska, J. and Schaper, E. (2015) ‘Statistical approaches to detecting and analyzing tandem repeats in genomic sequences’, Frontiers in Bioengineering and Biotechnology, 3(31). doi: 10.3389/fbioe.2015.00031.
• Anisimova, M. et al. (2015) ‘The SIB Swiss Institute of Bioinformatics’ resources : focus on curated databases’, Nucleic Acids Research, 44(D1), pp. D27–D37. doi: 10.1093/nar/gkv1310.
• Anisimova, M. (2015) ‘Darwin and Fisher meet at biotech : on the potential of computational molecular evolution in industry’, BMC Evolutionary Biology, 15, pp. 76–85. doi: 10.1186/s12862-015-0352-y.
• Zoller, S., Boskova, V. and Anisimova, M. (2015) ‘Maximum-likelihood tree estimation using codon substitution models with multiple partitions’, Molecular Biology and Evolution, 32(8), pp. 2208–2216. doi: 10.1093/molbev/msv097.
• Mirsky, A., Anisimova, M. and Kazandjian, L. (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. doi: 10.1093/molbev/msu340.
• Schaper, E., Gascuel, O. and Anisimova, M. (2014) ‘Deep conservation of human protein tandem repeats within the eukaryotes’, Molecular Biology and Evolution, 31(5), pp. 1132–1148. doi: 10.1093/molbev/msu062.
• Rech, G. E. et al. (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. doi: 10.1093/gbe/evu192.
• Schaper, E. and Anisimova, M. (2014) ‘The evolution and function of protein tandem repeats in plants’, New Phytologist, 206(1), pp. 397–410. doi: 10.1111/nph.13184.
• Dimitrieva, S. and 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). doi: 10.1371/journal.pone.0095034.

Books, peer-reviewed

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

Book chapters, peer-reviewed

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

Written conference contributions, peer-reviewed

• Aghaebrahimian, A., Anisimova, M. and Gil, M. (2022) ‘Ontology-aware biomedical relation extraction’, in Sojka, P. et al. (eds) Text, Speech, and Dialogue. Cham: Springer, pp. 160–171. doi: 10.1007/978-3-031-16270-1_14.
• Sima, A. C. et al. (2021) ‘Bio-SODA : enabling natural language question answering over knowledge graphs without training data’, in Proceedings of the 33rd SSDBM. Association for Computing Machinery, pp. 61–72. doi: 10.1145/3468791.3469119.
• Koroleva, A., Anisimova, M. and Gil, M. (2020) ‘Towards creating a new triple store for literature-based discovery’, in Lu, W. and Zhu, K. Q. (eds) Trends and Applications in Knowledge Discovery and Data Mining. PAKDD 2020. Cham: Springer, pp. 41–50. doi: 10.1007/978-3-030-60470-7_5.

Other publications

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

Oral conference contributions and abstracts

• Anisimova, M. (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, M. (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.
• Anisimova, M. (2016) ‘Evolution from mathematician to bioinformatician by natural selection’, in POST-DOC-DOC 2.0, Life Sciences, Schloss Au, Wädenswil, 2016.
• Osterhaus, A. D. M. E. et al. (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, M. (2015) ‘Disentangling tandem repeats, their evolution and roles in genomic sequences’, in EES Seminar Series LMU, München, Deutschland, 2015.
• Anisimova, M. (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, M. (2015) ‘Next generation comparative phylogenomics’, in StarOmics Symposium, Geneva, 2015.
• Anisimova, M. (2014) ‘Bioinformatique et génomique’, in Lycée de la Planta, Sion, 2014.
• Anisimova, M. (2014) ‘Visualisation of multiple sequence alignment and phylogeny’, in 2nd EMBO Visualizing Biological Data (VIZBI 2014), Heidelberg, 5-7 March 2014. Available at: https://www.vizbi.org/2014/Speakers/.

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