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| 36711453 | A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes. | bioRxiv | 2024 |
| 37398387 | BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. | bioRxiv | 2024 |
| 36331334 | A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist"). | G3 (Bethesda) | 2023 |
| 37244571 | MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes. | J Mol Biol | 2023 |
| 34056597 | GeneMark-HM: improving gene prediction in DNA sequences of human microbiome. | NAR Genom Bioinform | 2021 |
| 36303749 | StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. | Front Bioinform | 2021 |
| 33575650 | BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. | NAR Genom Bioinform | 2021 |
| 34823473 | TSEBRA: transcript selector for BRAKER. | BMC Bioinformatics | 2021 |
| 32275020 | Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis. | Parasite | 2020 |
| 33490913 | Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of <i>Chlamydomonas reinhardtii</i>. | iScience | 2020 |
| 32629900 | Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine. | Viruses | 2020 |
| 32440658 | GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. | NAR Genom Bioinform | 2020 |
| 29697742 | Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. | Brief Bioinform | 2019 |
| 31020555 | Whole-Genome Annotation with BRAKER. | Methods Mol Biol | 2019 |
| 30679363 | Toward unrestricted use of public genomic data. | Science | 2019 |
| 29659812 | The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). | Gigascience | 2018 |
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| 26559507 | BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. | Bioinformatics | 2016 |
| 25870408 | Identification of protein coding regions in RNA transcripts. | Nucleic Acids Res | 2015 |
| 24259430 | UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing. | Nucleic Acids Res | 2014 |
| 24990371 | Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. | Nucleic Acids Res | 2014 |
| 24908277 | Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. | Nat Biotechnol | 2014 |
| 24510847 | Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. | Curr Protoc Microbiol | 2014 |
| 24548928 | The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. | Nat Commun | 2014 |
| 23129300 | MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. | Bioinformatics | 2013 |
| 23649834 | Identification of the nature of reading frame transitions observed in prokaryotic genomes. | Nucleic Acids Res | 2013 |
| 23254332 | TrueSight: a new algorithm for splice junction detection using RNA-seq. | Nucleic Acids Res | 2013 |
| 23161689 | GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. | Nucleic Acids Res | 2013 |
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| 21186353 | The genome of woodland strawberry (Fragaria vesca). | Nat Genet | 2011 |
| 21829493 | The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. | PLoS One | 2011 |
| 21812137 | Guest editors' introduction to the special section on bioinformatics research and applications. | IEEE/ACM Trans Comput Biol Bioinform | 2011 |
| 21901742 | Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. | Curr Protoc Bioinformatics | 2011 |
| 21901741 | Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. | Curr Protoc Bioinformatics | 2011 |
| 21673094 | A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. | Mol Biol Evol | 2011 |
| 21318122 | Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences. | Methodol Comput Appl Probab | 2011 |
| 21435244 | Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. | BMC Genomics | 2011 |
| 20403810 | Ab initio gene identification in metagenomic sequences. | Nucleic Acids Res | 2010 |
| 21143775 | 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. | BMC Genomics | 2010 |
| 20852019 | The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. | Plant Cell | 2010 |
| 20547848 | Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). | Proc Natl Acad Sci U S A | 2010 |
| 20438648 | Bacillus anthracis genome organization in light of whole transcriptome sequencing. | BMC Bioinformatics | 2010 |
| 20556861 | Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. | J Bioinform Comput Biol | 2010 |
| 19082552 | In silico identification of genes in bacteriophage DNA. | Methods Mol Biol | 2009 |
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| 18757608 | Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. | Genome Res | 2008 |
| 17240398 | Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. | J Theor Biol | 2007 |
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