Prof. Dr. Maria Anisimova

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 / Projektleiter:in / laufend
• REFRACT – Repeat protein Function, Refinement, Annotation and Classification of Topologies / Projektleiter:in / laufend
• AI for colorectal cancer: towards the improved CMS classification and interpretability / Projektleiter:in / abgeschlossen
• Die Exploration der Gen-Harmonisierung / Teammitglied / abgeschlossen
• Computational literature-based natural product drug discovery / Teammitglied / abgeschlossen
• The effect of programmed ribosomal frameshifting on codon usage bias / Projektleiter:in / abgeschlossen
• Frequentist estimation of the evolutionary history of sequences with substitutions and indels / Projektleiter:in / abgeschlossen
• Positive selection detection of genome from Ralstonia bacterium / Projektleiter:in / abgeschlossen
• Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (Bio-SODA) / Teammitglied / abgeschlossen
• Exploring the silent fitness landscape / Projektleiter:in / abgeschlossen
• Discovering evolutionary innovations by assessing variation and natural selection in protein tandem repeats / Projektleiter:in / abgeschlossen
• Fast joint estimation of alignment and phylogeny from genomics sequences in a frequentist framework / Projektleiter:in / abgeschlossen

Publikationen

• 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

• 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

• 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), S. 321-336.

  Verfügbar unter: 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), S. 307-318.

  Verfügbar unter: 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), S. 409-440.

  Verfügbar unter: 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).

  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

• 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, S. 240-248.

  Verfügbar unter: 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).

  Verfügbar unter: 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).

  Verfügbar unter: 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).

  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

• 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

• 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

• 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

• 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), 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

• 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

• 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), S. 204-215.

  Verfügbar unter: 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).

  Verfügbar unter: 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), S. 3487-3498.e10.

  Verfügbar unter: 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, S. 66-82.

  Verfügbar unter: 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), S. 553-564.

  Verfügbar unter: 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, S. 76-85.

  Verfügbar unter: 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), S. 2208-2216.

  Verfügbar unter: 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).

  Verfügbar unter: 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), S. D27-D37.

  Verfügbar unter: 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), S. 3051-3053.

  Verfügbar unter: 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), S. 806-819.

  Verfügbar unter: 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), S. 1132-1148.

  Verfügbar unter: 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), S. 397-410.

  Verfügbar unter: 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).

  Verfügbar unter: https://doi.org/10.1371/journal.pone.0095034

• 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

• 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

• Kosiol, Carolin; Anisimova, Maria,

  2019.

  Selection acting on genomes

  .

  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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• Anisimova, Maria,

  2016.

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

  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.

  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), S. 2368-2379.

  Verfügbar unter: https://doi.org/10.1093/gbe/evu192

• 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.

  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.

  Verfügbar unter: https://www.vizbi.org/2014/Speakers/

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