NLP-inspired structural pattern recognition in chemical application. - Julia Sidorova; Maria Anisimova (Pattern Recognit. Lett., 2014)

TRAL: tandem repeat annotation library. - Elke Schaper; Alexander Korsunsky; Julija Pecerska; Antonio Messina; Riccardo Murri; Heinz Stockinger; Stefan Zoller; Ioannis Xenarios; Maria Anisimova (Bioinform., 2015)

Progressive multiple sequence alignment with indel evolution. - Massimo Maiolo; Xiaolei Zhang; Manuel Gil; Maria Anisimova (BMC Bioinform., 2018)

Enabling semantic queries across federated bioinformatics databases. - Ana Claudia Sima; Tarcisio Mendes de Farias; Erich Zbinden; Maria Anisimova; Manuel Gil; Heinz Stockinger; Kurt Stockinger; Marc Robinson-Rechavi; Christophe Dessimoz (Database J. Biol. Databases Curation, 2019)

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (SSDBM, 2021)

ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process. - Massimo Maiolo; Lorenzo Gatti; Diego Frei; Tiziano Leidi; Manuel Gil; Maria Anisimova (BMC Bioinform., 2021)

TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner. - Matteo Delucchi; Paulina Näf; Spencer Bliven; Maria Anisimova (Frontiers Bioinform., 2021)

Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer. - Max A. Verbiest; Matteo Delucchi; Tugce Bilgin Sonay; Maria Anisimova (Frontiers Bioinform., 2021)

Querying knowledge graphs in natural language. - Shiqi Liang; Kurt Stockinger; Tarcisio Mendes de Farias; Maria Anisimova; Manuel Gil (J. Big Data, 2021)

Attitude in diplomatic speeches: a pilot study. - Maria Anisimova; Sárka Zikánová (ITAT, 2022)

Ontology-Aware Biomedical Relation Extraction. - Ahmad Aghaebrahimian; Maria Anisimova; Manuel Gil (TSD, 2022)

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (Distributed Parallel Databases, 2022)

Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects. - Andreas Lardos; Ahmad Aghaebrahimian; Anna Koroleva; Julia Sidorova; Evelyn Wolfram; Maria Anisimova; Manuel Gil (Frontiers Bioinform., 2022)

Problematic Cases of Attitude Annotation in Diplomatic Speeches. - Maria Anisimova; Sárka Zikánová (ITAT, 2024)

Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction. - Gholamhossein Jowkar; Julija Pecerska; Manuel Gil; Maria Anisimova (BMC Bioinform., 2024)

Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms. - Feifei Xia; Max A. Verbiest; Oxana Lundström; Tugce Bilgin Sonay; Michael Baudis; Maria Anisimova (Briefings Bioinform., 2025)