Prof. Dr. Maria Anisimova

Personal profile

Management role

• Director of Department, Bioinformatics, Computational Genomics
• Head of Research/Focus Area, Bioinformatics, Computational Genomics

Position at the ZHAW

Head of Research Center for Bioinformatics, Lecturer, SIB group leader

www.zhaw.ch/en/lsfm/institutes-centres/icls/bioinformatics/

Professional development teaching

Bioinformatics for Beginners

Expertise and research interests

Stochastic modeling and simulation for genomic data
Model-based classification, prediction and hypothesis testing
Algorithms for genomic sequence analysis
Bio-statistical model selection and hypothesis testing based on molecular sequences
Applied computational genomics for medicine, forensics, ecology and agriculture

Educational background

CAS Hochschuldidaktik (2018), PHZH - Pädagogische Hochschule Zürich
PhD in Statistical Genomics (2003) University College London, UK
MRes in Modeling Biological Complexity (2000) University College London, UK
MSci in Mathematics and IT (1993) Pedagogical University of Nizhny Novgorod, Russia
Certified high school teacher (1993) Pedagogical University of Nizhny Novgorod, Russia

My research group focuses on methods for computation genomics, evolution and semantic web technologies - with applications to a variety of problems in pharmacology, medicine, forensics, ecology and agriculture. We are interested in the theoretical aspects of modeling molecular evolution as well as data-driven applications of new methodologies, particularly the computational methods to study the process of gene and genome evolution and the process of adaptive genetic change. Data from transcriptomics, proteomics, metabolomics, metagenomics and epigenomics are growing rapidly and have serious impact on genomics and our understanding of molecular cell biology and its various effects on the phenotype and disease. But the challenge of understanding the dynamics of such large-system data can only be met through an integration of organism, molecular, and mathematical disciplines. New techniques need to be developed for discovering complex patterns from multi-faced systems biology data.

Professional milestones

From December 2021: Professor in Computational Genomics
2015 - now: Research Group leader, Swiss Institute of Bioinformatics (SIB), Switzerland
2014 - now: Research Group leader, ZHAW Wädenswil, Switzerland
2007 - 2014: Senior research fellow and lecturer, Computer Science Department, ETH Zürich, Switzerland
2005 - 2007: Postdoctoral researcher, Biology Department, University College London, UK
2003 - 2004: Postdoctoral researcher, LIRMM-CNRS, University of Montpellier II, France
1997 - 1999: Head of maths and IT, teacher, Bellerbys College London, Study Group International, UK
1993 - 1997: Assistant lecturer, School of Geometry, Nizhny Novgorod Pedagogical State University, Russia

Membership of networks

• Swiss Institute of Bioinformatics
• REFRACT MSCA RISE PROJECT 2019 (H2020 EU GA N 823886)
• PhD Network in Data Science
• European COST Action BM1405 "Non-globular proteins - from sequence to structure, function & application in molecular physiopathology"

Projects

• AI for colorectal cancer: towards the improved CMS classification and interpretability / Project leader / Project ongoing
• 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
• 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

• 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

• 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

• 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

• 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.

  ACM.

  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

• 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/

• 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/

Publications before appointment at the ZHAW

All publications can be found on Google Scholar:
scholar.google.com/citations

*** BOOKS ****************************

Anisimova, M. (Ed.) 2012. Evolutionary Genomics: statistical and computational methods Springer (Humana Press):
vol 1: ISBN 978-1-61779-581-7
vol 2: ISBN 978-1-61779-584-8

*** BOOK CHAPTERS and REVIEWS *********

Kosiol C. and M. Anisimova 2012. Methods for detecting natural selection in protein-coding genes in "Evolutionary Genomics: statistical and computational methods" vol. 2 , ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer link

Anisimova, M. 2012. Parametric models of codon evolution in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press

Anisimova, M. and D. Liberles 2012. Detecting and understanding natural selection, in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press

Roth, A., M. Anisimova, and G.M. Cannarozzi 2012. Measuring codon usage bias, in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press

Anisimova*, M., G.M. Cannarozzi* , and D.A. Liberles* 2010. Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends Evol. Biol. 2(1): e7


*** EDITORIALS ************************

Anisimova, M., D. A. Liberles, H. Philippe, J. Provan, T. Pupko, and A. von Haeseler 2013. State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol. Biol. 13:161

Anisimova, M. 2012. Preface to “Evolutionary genomics: statistical and computational methods” (2 vols), ed. Anisimova, in Meth Mol Biol, Springer


*** PEER_REVIEWED RESEARCH ARTICLES ***

Sidorova, J. and M. Anisimova 2014. NLP-inspired structural pattern recognition in chemical application. Pattern Recognition Letters 45:11–16

Gil*, M., M.S. Zanetti*, S. Zoller, and M Anisimova 2013. CodonPhyML: Fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol 30(6):1270-80

Szalkowski, A., and M. Anisimova 2013. Graph-based modeling of tandem repeats improves global multiple sequence alignment. Nucl Acids Res 41(17):e162

Peeters, N., S. Carrère, M. Anisimova, L. Plener, A.C. Cazalé, S. Genin 2013. Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics 14:859

Schirrmeister, B.E., D.A. Dalquen, M. Anisimova and H.C. Bagheri 2012. Gene copy number variation and its significance in cyanobacterial phylogeny. BMC Microbiology 2:177

Schaper, E., A.V. Kajava, A. Hauser, and M. Anisimova 2012. Repeat or not repeat?—Statistical validation of tandem repeat prediction in genomic sequences Nucl. Acids Res. 40 (20): 10005-10017

Anisimova, M., M. Gil, JF. Dufayard, C. Dessimoz, O. Gascuel 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60:685–699

Schirrmeister B. E., M. Anisimova, A. Antonelli, H. C. Bagheri 2011. Evolution of cyanobacterial morphotypes: taxa required for improved phylogenomic approaches. Communicative & Integrative Biology 4(4): 424–427

Szalkowski A., and M. Anisimova 2011. Markov models of amino acid substitution to study proteins with intrinsically disordered regions. PLoS One 6(5): e20488

Balakirev E.S., M. Anisimova, and F.J. Ayala 2011. Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster. PLoS One 6(7): e22613

Remigi P., M. Anisimova, A. Guidot, S. Genin and N. Peeters. 2011. Functional diversification of the GALA type-three effector family contributes to Ralstonia solanacearum adaptation on several plant hosts. New Phytologist 192(4): 976–987

Dalquen D. A, M. Anisimova, G. Gonnet, and C. Dessimoz 2011. ALF - A simulation framework for genome evolution. Mol Biol Evol 29(4): 1115-1123

Wang M, M. Kapralov, and M. Anisimova 2011. Co-evolution of amino acid residues in the key photosynthetic enzyme RuBisCo in land plants. BMC Evol Biol 11:266

Guindon, S., JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk and O. Gascuel 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Syst. Biol. 59(3):307-321

Dimitrieva, S. and M. Anisimova 2010. PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources. Trends Evol. Biol. 2(1): e1

Anisimova, M. and C. Kosiol 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 26(2):255-271

Kajava, A.V., M. Anisimova, and N. Peeters 2008. Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria? PLoS One 3(2): e1694.

Anisimova, M. and Z. Yang 2007. Multiple hypotheses testing to detect adaptive protein evolution affecting individual branches and sites. Mol. Biol. Evol. 24:1219-1228

Anisimova, M., J.P. Bielawski, K. Dunn and Z. Yang 2007. Phylogenomic analysis of natural selection pressure in Streptococcus. BMC Evol. Biol. 7:154-167

Anisimova, M. and D. A. Liberles. 2007 The quest for natural selection in the age of comparative genomics. Heredity 99:567-579

Anisimova, M. and O. Gascuel. 2006. Approximate likelihood ratio test for branches: a fast, accurate and powerful alternative. Syst. Biol. 55(4):539-552

Balakirev, E.S., M. Anisimova, and F.J. Ayala 2006. Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. J. Mol. Evol. 62: 496-510

Anisimova, M. and Z. Yang 2004. Molecular evolution of HDV antigen gene: recombination or positive selection? J. Mol. Evol. 59: 815-826

Anisimova, M., R. Nielsen, and Z. Yang 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236

Anisimova, M., J. P. Bielawski, and Z. Yang 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19:950-958

Anisimova, M., J. P. Bielawski, and Z. Yang 2001. Accuracy and power of the likelihood ratio test to detect adaptive molecular evolution. Mol. Biol. Evol. 18:1585-1592

Other publications

Teaching:

MSc ACLS, semester course "Mathematical modeling" (Stochastic processes)
MSc ACLS, semester course "Computational Genomics" (Track 1 and Track 2)
PhD network in Data Science, semester course "Inferential statistics for data scientists" (UZH-ETHZ-ZHAW)
PhD network in Plant Sciences, short course "Molecular Evolution and Phylogenetics"

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