| BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database T Brůna, KJ Hoff, A Lomsadze, M Stanke, M Borodovsky NAR genomics and bioinformatics 3 (1), lqaa108, 2021 | 878 | 2021 |
| GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins T Brůna, A Lomsadze, M Borodovsky NAR genomics and bioinformatics 2 (2), lqaa026, 2020 | 256 | 2020 |
| TSEBRA: transcript selector for BRAKER L Gabriel, KJ Hoff, T Brůna, M Borodovsky, M Stanke Bmc Bioinformatics 22, 1-12, 2021 | 89 | 2021 |
| BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA L Gabriel, T Brůna, KJ Hoff, M Ebel, A Lomsadze, M Borodovsky, ... Biorxiv, 2023 | 33 | 2023 |
| Chameleon 2: an improved graph-based clustering algorithm T Barton, T Bruna, P Kordik ACM Transactions on Knowledge Discovery from Data (TKDD) 13 (1), 1-27, 2019 | 28 | 2019 |
| GeneMark-ETP: automatic gene finding in eukaryotic genomes in consistency with extrinsic data T Bruna, A Lomsadze, M Borodovsky BioRxiv, 2023 | 13 | 2023 |
| A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”) T Brůna, R Aryal, O Dudchenko, DJ Sargent, D Mead, M Buti, A Cavallini, ... G3 13 (2), jkac289, 2023 | 9 | 2023 |
| Galba: genome annotation with miniprot and AUGUSTUS T Brůna, H Li, J Guhlin, D Honsel, S Herbold, M Stanke, N Nenasheva, ... BMC bioinformatics 24 (1), 327, 2023 | 7 | 2023 |
| Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii WMM El-Sayed, AL Gombolay, P Xu, T Yang, Y Jeon, S Balachander, ... Iscience 24 (1), 2021 | 7 | 2021 |
| The BRAKER3 genome annotation pipeline L Gabriel, KJ Hoff, T Bruna, A Lomsadze, M Borodovsky, M Stanke Plant and Animal Genomes Conference 30, 2023 | 2 | 2023 |
| Unsupervised algorithms for automated gene prediction in novel eukaryotic genomes T Bruna Georgia Institute of Technology, 2022 | 2 | 2022 |
| Mocham: robust hierarchical clustering based on multi-objective optimization T Barton, T Bruna, P Kordik 2016 IEEE 16th International Conference on Data Mining Workshops (ICDMW …, 2016 | 2 | 2016 |
| The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus SH Brainard, DM Sanders, T Bruna, S Shu, JC Dawson Plant Biotechnology Journal 22 (2), 472-483, 2024 | 1 | 2024 |
| Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to BRAKER, Galba, and TSEBRA T Brůna, L Gabriel, KJ Hoff arXiv preprint arXiv:2403.19416, 2024 | | 2024 |
Mark BorodovskyRegents' Professor, Georgia TechVerified email at gatech.edu
