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Identification of protein coding regions in RNA transcripts

Nucleic acids research, 2015-07, Vol.43 (12), p.e78-e78

2015

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Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

Genome research, 2018-07, Vol.28 (7), p.1079-1089

2018

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TSEBRA: transcript selector for BRAKER

BMC bioinformatics, 2021-11, Vol.22 (1), p.1-566, Article 566

2021

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Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES

Current Protocols in Bioinformatics, 2011-09, Vol.35 (1), p.4.6.1-4.6.10

2011

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Nature biotechnology, 2014-07, Vol.32 (7), p.656-662

2014

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Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Proceedings of the National Academy of Sciences - PNAS, 2010-06, Vol.107 (26), p.11889-11894

2010

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genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

Genome biology, 2012-05, Vol.13 (5), p.R39-R39, Article R39

2012

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Dynamic Systems Models: New Methods of Parameter and State Estimation

1st ed. 2016, 2016

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Ab initio gene identification in metagenomic sequences

Nucleic acids research, 2010-07, Vol.38 (12), p.e132-e132

2010

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StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes

Frontiers in bioinformatics, 2021-12, Vol.1, p.704157-704157

2021

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GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

NAR genomics and bioinformatics, 2020-06, Vol.2 (2)

2020

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Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

BMC bioinformatics, 2006-03, Vol.7 (1), p.178-178, Article 178

2006

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Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine

Viruses, 2020-06, Vol.12 (7), p.710

2020

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A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)

G3 : genes - genomes - genetics, 2023-02, Vol.13 (2)

2023

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Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

Nucleic acids research, 2014-09, Vol.42 (15), p.e119-e119

2014

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Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis

Parasite (Paris), 2020, Vol.27, p.24

2020

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Whole-Genome Annotation with BRAKER

Methods in molecular biology (Clifton, N.J.), 2019-01, Vol.1962, p.65

2019

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BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

Bioinformatics, 2016-03, Vol.32 (5), p.767-769

2016

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Bacillus anthracis genome organization in light of whole transcriptome sequencing

BMC bioinformatics, 2010-04, Vol.11 Suppl 3 (S3), p.S10-S10, Article S10

2010

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Exonization of the LTR transposable elements in human genome

BMC genomics, 2007-08, Vol.8 (1), p.291-291, Article 291

2007

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cag, a Pathogenicity Island of Helicobacter pylori, Encodes Type I-Specific and Disease-Associated Virulence Factors

Proceedings of the National Academy of Sciences - PNAS, 1996-12, Vol.93 (25), p.14648-14653

1996

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GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

Genome research, 2024-05, Vol.34 (5), p.757-768

2024

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MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes

Journal of molecular biology, 2023-07, Vol.435 (14), p.168159-168159, Article 168159

2023

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Identification of Proteins Associated with Murine Cytomegalovirus Virions

Journal of Virology, 2004-10, Vol.78 (20), p.11187-11197

2004

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Identification of protein coding regions in RNA transcripts

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

TSEBRA: transcript selector for BRAKER

Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

Dynamic Systems Models: New Methods of Parameter and State Estimation

Ab initio gene identification in metagenomic sequences

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes

GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants

Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”)

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis

Whole-Genome Annotation with BRAKER

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Exonization of the LTR transposable elements in human genome

cag, a Pathogenicity Island of Helicobacter pylori, Encodes Type I-Specific and Disease-Associated Virulence Factors

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes

Identification of Proteins Associated with Murine Cytomegalovirus Virions

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