Whole-Genome Annotation with BRAKER
Hoff, Katharina J, Lomsadze, Alexandre, Borodovsky, Mark, Stanke, Mario
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2019)
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2019)
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Journal Article
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Hoff, Katharina J, Lange, Simone, Lomsadze, Alexandre, Borodovsky, Mark, Stanke, Mario
Published in Bioinformatics (01.03.2016)
Published in Bioinformatics (01.03.2016)
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Journal Article
TSEBRA: transcript selector for BRAKER
Gabriel, Lars, Hoff, Katharina J, Brůna, TomáÅ, Borodovsky, Mark, Stanke, Mario
Published in BMC bioinformatics (25.11.2021)
Published in BMC bioinformatics (25.11.2021)
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Journal Article
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
Gabriel, Lars, Brůna, Tomáš, Hoff, Katharina J, Ebel, Matthis, Lomsadze, Alexandre, Borodovsky, Mark, Stanke, Mario
Published in Genome research (01.05.2024)
Published in Genome research (01.05.2024)
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Journal Article
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria
Philippe, Hervé, Poustka, Albert J., Chiodin, Marta, Hoff, Katharina J., Dessimoz, Christophe, Tomiczek, Bartlomiej, Schiffer, Philipp H., Müller, Steven, Domman, Daryl, Horn, Matthias, Kuhl, Heiner, Timmermann, Bernd, Satoh, Noriyuki, Hikosaka-Katayama, Tomoe, Nakano, Hiroaki, Rowe, Matthew L., Elphick, Maurice R., Thomas-Chollier, Morgane, Hankeln, Thomas, Mertes, Florian, Wallberg, Andreas, Rast, Jonathan P., Copley, Richard R., Martinez, Pedro, Telford, Maximilian J.
Published in Current biology (03.06.2019)
Published in Current biology (03.06.2019)
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Journal Article
Galba: genome annotation with miniprot and AUGUSTUS
Brůna, Tomáš, Li, Heng, Guhlin, Joseph, Honsel, Daniel, Herbold, Steffen, Stanke, Mario, Nenasheva, Natalia, Ebel, Matthis, Gabriel, Lars, Hoff, Katharina J
Published in BMC bioinformatics (31.08.2023)
Published in BMC bioinformatics (31.08.2023)
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Journal Article
Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior
Errbii, Mohammed, Keilwagen, Jens, Hoff, Katharina J., Steffen, Raphael, Altmüller, Janine, Oettler, Jan, Schrader, Lukas
Published in Molecular ecology (01.12.2021)
Published in Molecular ecology (01.12.2021)
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Journal Article
VARUS: sampling complementary RNA reads from the sequence read archive
Stanke, Mario, Bruhn, Willy, Becker, Felix, Hoff, Katharina J
Published in BMC bioinformatics (08.11.2019)
Published in BMC bioinformatics (08.11.2019)
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Journal Article
Orphelia: predicting genes in metagenomic sequencing reads
Hoff, Katharina J., Lingner, Thomas, Meinicke, Peter, Tech, Maike
Published in Nucleic acids research (01.07.2009)
Published in Nucleic acids research (01.07.2009)
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Journal Article
Neutrophil-derived reactive agents induce a transient SpeB negative phenotype in Streptococcus pyogenes
Shumba, Patience, Sura, Thomas, Moll, Kirsten, Chakrakodi, Bhavya, Tölken, Lea A, Hoßmann, Jörn, Hoff, Katharina J, Hyldegaard, Ole, Nekludov, Michael, Svensson, Mattias, Arnell, Per, Skrede, Steinar, Norrby-Teglund, Anna, Siemens, Nikolai
Published in Journal of biomedical science (10.07.2023)
Published in Journal of biomedical science (10.07.2023)
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Journal Article
Standards recommendations for the Earth BioGenome Project
Lawniczak, Mara K N, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Marques Bonet, Tomas, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, Richards, Stephen
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2022)
Published in Proceedings of the National Academy of Sciences - PNAS (25.01.2022)
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Journal Article
Finding the missing honey bee genes: lessons learned from a genome upgrade
Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg J, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin F A, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Vaerenbergh, Matthias Van, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A
Published in BMC genomics (30.01.2014)
Published in BMC genomics (30.01.2014)
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Journal Article
The genomic basis of evolutionary differentiation among honey bees
Fouks, Bertrand, Brand, Philipp, Nguyen, Hung N, Herman, Jacob, Camara, Francisco, Ence, Daniel, Hagen, Darren, Hoff, Katherina J, Nachweide, Stefanie, Romoth, Lars, Walden, Kimberly Ko, Guigo, Roderic, Stanke, Mario, Narzisi, Giuseppe, Yandell, Mark, Robertson, Hugh M, Koeniger, Nikolaus, Chantawannakul, Panuwan, Schatz, Michael C, Worley, Kim C, Robinson, Gene E, Elsik, Christine G, Rueppell, Olav
Published in Genome research (01.07.2021)
Published in Genome research (01.07.2021)
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Journal Article
Gene prediction in metagenomic fragments: a large scale machine learning approach
Hoff, Katharina J, Tech, Maike, Lingner, Thomas, Daniel, Rolf, Morgenstern, Burkhard, Meinicke, Peter
Published in BMC bioinformatics (28.04.2008)
Published in BMC bioinformatics (28.04.2008)
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Journal Article
The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads
Wöhner, Thomas W., Emeriewen, Ofere F., Wittenberg, Alexander H.J., Schneiders, Harrie, Vrijenhoek, Ilse, Halász, Júlia, Hrotkó, Károly, Hoff, Katharina J., Gabriel, Lars, Lempe, Janne, Keilwagen, Jens, Berner, Thomas, Schuster, Mirko, Peil, Andreas, Wünsche, Jens, Kropop, Stephan, Flachowsky, Henryk
Published in Genomics (San Diego, Calif.) (01.11.2021)
Published in Genomics (San Diego, Calif.) (01.11.2021)
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Journal Article
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
Shaidullina, Elvira R, Schwabe, Michael, Rohde, Thomas, Shapovalova, Valeria V, Dyachkova, Marina S, Matsvay, Alina D, Savochkina, Yuliya A, Shelenkov, Andrey A, Mikhaylova, Yulia V, Sydow, Katharina, Lebreton, François, Idelevich, Evgeny A, Heiden, Stefan E, Becker, Karsten, Kozlov, Roman S, Shipulin, German A, Akimkin, Vasiliy G, Lalk, Michael, Guenther, Sebastian, Zautner, Andreas E, Bohnert, Jürgen A, Mardanova, Ayslu M, Bouganim, Ruth, Marchaim, Dror, Hoff, Katharina J, Schaufler, Katharina, Edelstein, Mikhail V
Published in Genome medicine (13.02.2023)
Published in Genome medicine (13.02.2023)
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Journal Article
An initial comparative genomic autopsy of wasting disease in sea stars
Ruiz‐Ramos, Dannise V., Schiebelhut, Lauren M., Hoff, Katharina J., Wares, John P., Dawson, Michael N
Published in Molecular ecology (01.03.2020)
Published in Molecular ecology (01.03.2020)
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