| 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 | 1406 | 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 | 398 | 2020 |
| TSEBRA: transcript selector for BRAKER L Gabriel, KJ Hoff, T Brůna, M Borodovsky, M Stanke BMC bioinformatics 22, 1-12, 2021 | 185 | 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, ... Genome Research 34 (5), 769-777, 2024 | 167 | 2024 |
| BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP L Gabriel, T Brůna, KJ Hoff, M Ebel, A Lomsadze, M Borodovsky, ... AUGUSTUS and TSEBRA. bioRxiv 10 (10.1101), 2023.06, 2023 | 58 | 2023 |
| GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes T Brůna, A Lomsadze, M Borodovsky Genome Research 34 (5), 757-768, 2024 | 43* | 2024 |
| 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 | 35 | 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 | 35 | 2019 |
| 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 | 14 | 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 | 10 | 2021 |
| Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean MJC Espina, JT Lovell, J Jenkins, S Shu, A Sreedasyam, BD Jordan, ... The Plant Journal 120 (3), 1221-1235, 2024 | 4 | 2024 |
| 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 | 3 | 2024 |
| The BRAKER3 genome annotation pipeline L Gabriel, KJ Hoff, T Bruna, A Lomsadze, M Borodovsky, M Stanke Plant and Animal Genomes Conference 30, 2023 | 3 | 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 |
| Conservative taxonomy and quality assessment of giant virus genomes with GVClass TM Pitot, T Brůna, F Schulz npj Viruses 2 (1), 60, 2024 | 1 | 2024 |
| Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes H Lee, JS Stai, Q Xu, T Hewavithana, R Batra, A Liu, BD Jordan, ... bioRxiv, 2024.09. 03.611065, 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 TechCorreu electrònic verificat a gatech.edu
