PD Dr. Katharina Hoff

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Bioinformatisches Praktikum (Vorlesung/Übung, Moodle-Course)

Bioinformatisches Praktikum für Studierende der Humanbiologie (Moodle-Course)

Statistik I Vorlesung (Vorlesung/Übung, Moodle-Course)

You find an overview of courses within the project "Data Competency" at https://math-inf.uni-greifswald.de/forschung/informatik-und-logik/bioinformatik/datenkompetenz/

At University of Greifswald, I gave the following courses:

• Bioinformatisches Praktikum (Vorlesung & Übung)
• Praxis des Programmierens (Übung)
• Statistik für Studierende der Pharmazie, Geographie und Landschaftsökologie (Vorlesung & Übung)
• Einführung in die Informatik (Übung)
• Datenbanken (Übung)
• Genomanalyse (Teile von Vorlesung & Übung)
• R-Kurs
• Python-Kurs
• LaTeX-Kurs
• Seminar Genomannotation

I gave the following courses at other institutions:

• Genome Annotation
• Methods Course Bioinformatics
• Typesetting Scientific Presentations with the LaTeX-Beamer Class
• Bioinformatics Tutorial
• Biotechnology Tutorial

Since 2007, I am teaching the usage of R, a language for statistics and graphics, for various audiences.

*) Ich veröffentliche alle Evaluationsergebnisse ohne handschriftliche Kommentare. Die Evaluationsergebnisse sind im Intranet der Universität Greifswald erreichbar.

Gene Finding, Biotechnology, Diversity, Academia @Amd Lab Podcast , an interview on my research with Dr. Ahmad Nazzal (Youtube Link)

N. Nenasheva, C. Pitzschel, C. N. Webster, A. Hart, J. L. Wegrzyn, M. M. Bengtsson, K. J. Hoff
Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade
arXiv (2024) https://doi.org/10.48550/arXiv.2410.05467

L. Gabriel, F. Becker, K. J. Hoff, M. Stanke
Tiberius: End-to-End Deep Learning mit an HMM for Gene Prediction
bioRxiv (2024) https://doi.org/10.1101/2024.07.21.604459

T. Bruna, L. Gabriel, K. J. Hoff
Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to BRAKER, Galba, and TSEBRA
arXiv (2024) https://doi.org/10.48550/arXiv.2403.19416

M. M. Sheffer, L. Zander, B. Schulze, P. Mouginot, T. Naef, J. Kreyling, R. G. Gillespie, K. J. Hoff, S. Prost, H. Krehenwinkel, G. Uhl
Rapid ecological and evolutionary divergence during a poleward range expansion
bioRxiv (2021) https://doi.org/10.1101/2021.11.04.467261

S. Richter, S. Kind, T. Oberhänsli, M. Schneider, N. Nenasheva, K. Hoff, J. Keilwagen, I.-K. Yeon, V. Philion, S. Moriya, H. Flachkowsky, A. Patocchi, T. W. Wöhner
Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating type locus
Frontiers in Plant Science (2024) 15, https://doi.org/10.3389/fpls.2024.1437132

P. H. Schiffer, P. Natsidis, D. J. Leite, H. E. Robertson, F. Lapraz, F. Marlétaz, B. Fromm, L. Baudry, F. Simpson, E. Høye, A.-C. Zakrzewski, P. Kapli, K. J. Hoff, S. Mueller, M. Marbouty, H. Marlow, R. R. Copley, R. Koszul, P. Sarkies, M. J. Telford
Insights into early animal evolution form the genome of the xenacoelomorph worm Xenoturbella bocki
eLife (2024),  https://doi.org/10.7554/eLife.94948, Preprint on [bioRxiv]

A. Catalan, D. Gygax, L. Rodriguez-Montes, T. Hinzke, K. Hoff, P. Duchen
Two novel genomes of fireflies with different degrees of sexual dimorphism reveal insights into sex-biased gene expression and dosage compensation
Communications Biology (2024) 7:906, https://doi.org/10.1038/s42003-024-06550-6

L. Gabriel, T. Bruna, K.J. Hoff, M. Ebel, A. Lomsadze, M. Borodovsky, M. Stanke
BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
Genome Research (2024), https://www.genome.org/cgi/doi/10.1101/gr.278090.123 Preprint on [bioRxiv]

R. Siebers, D. Schultz, M. S. Farza, A. Brauer, D. Zühlke, P. Mücke, F. Wang, J. Bernhardt, H. Teeling, D. Becher, K. Riedel, I. V. Kirstein, K. Wiltshire, K. J. Hoff, T. Schweder, T. Urich, M. M. Bengtsson
Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria
FEMS Microbiology Ecology (2024), fiae037, https://doi.org/10.1093/femsec/fiae037

L. A. Tölken, A. D. Paulikat, L. H. Jachmann, A. Reder, M. Gesell Salazar, L. M. Palma Medina, S. Michalik, U. Völker, M. Svensson, A. Norrby-Teglund, K. J. Hoff, M. Lammers, N. Siemens 
Reduced interleukin-18 secretion by human monocytic cells in response to infections with hyper-virulent Streptococcus pyogenes
Journal of Biomedical Science (2024), 31:26, https://doi.org/10.1186/s12929-024-01014-9.

T. W. Wöhner, O. F. Emeriewen, A. H. J. Wittenberg, K. Nijbroek, R. P. Wang, E.-J. Blom, H. Schneiders, J. Keilwagen, T. Berner, K. J. Hoff, L. Gabriel, H. Thierfeldt, O. Almolla, L. Barchi, M. Schuster, J. Lempe, A. Peil, H. Flachowsky
The structure of the tetraploid sour cherry ‘Schattenmorelle’ (Prunus cerasus L.) genome reveals insights into its segmental allopolyploid nature
Frontiers in Plant Science (2023), 14 https://doi.org/10.3389/fpls.2023.1284478. Preprint on [bioRxiv]

L. M. Schiebelhut, M. B. DeBiasse, L. Gabriel, K. J. Hoff, M. N. Dawson
A Reference Genome for Ecological Restoration of the Sunflower Sea Star, Pycnopodia helianthoides
Journal of Heredity (2023), esad054 https://doi.org/10.1093/jhered/esad054

T. Brůna, H. Li, J. Guhlin, D. Honsel, S. Herbold, M. Stanke, N. Nenasheva, M. Ebel, L. Gabriel, K. J. Hoff
Galba: genome annotation with miniprot and AUGUSTUS
BMC Bioinformatics (2023) 24:327 https://doi.org/10.1186/s12859-023-05449-z

E. R. Shaidullina, M. Schwabe, T. Rohde, V. V. Shapovalova, M. S. Dyachkova, A. D. Matsvay, Y. A. Savochkina, A. A. Shelenkov, Y. V. Mikhaylova, K. Sydow, F. Lebreton, E. A. Idelevich, S. E. Heiden, K. Becker, R. S. Kozlov, G. A. Shipulin, V. G. Akimkin, M. Lalk, S. Guenther, A. E. Zautner, J. A. Bohnert, A. M. Mardanova, R. Bouganim, D. Marchaim, K. J. Hoff, K. Schaufler, M. V. Edelstein
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
Genome Medicine (2023) 15:9 https://doi.org/10.1186/s13073-023-01159-6

P. Shumba, T. Sura, K. Moll, B. Chakrakodi, L.A. Tölken, J. Hoßmann, K.J. Hoff, O. Hyldegaard, M. Svensson, P. Anrell, S. Skrede, A. Norrby-Teglund, N. Siemens.
Neutrophil-derived reactive agents induce a transient SpeB negative phenotype in Streptococcus pyogenes
Journal of Biomedical Science (2023) 30:52 https://doi.org/10.1186/s12929-023-00947-x

M. K. N. Lawniczak, R. Durbin, P. Flicek, K. Lindblad-Toh, X. Wei, J. M. Archibald, W. J. Baker, K. Belov, M. L. Blaxter, T. Marques Bonet, A. K. Childers, J. A. Coddington, K. A. Crandall, A. J. Crawford, R. P. Davey, F. Di Palma, Q. Fang, W. Haerty, N. Hall, K. J. Hoff, K. Howe, E. D. Jarvis, W. E. Johnson, R.N. Johnson, P. J. Kersey, X. Liu, J. V. Lopez, E. W. Myers, O. Vinnere Pettersson, A. M. Phillippy, M. F. Poelchau, K. D. Pruitt, A. Rhie, J. C. Castilla-Rubio, S. Kumar Sahu, N. A. Salmon, P. S. Soltis, D. Swarbreck, F. Thibaud-Nissen, S. Wang, J. L. Wegrzyn, G. Zhang, H. Zhang, H. A. Lewin, S. Richards.
Standards recommendations for the Earth BioGenome Project
Proceedings of the National Academy of Sciences of the United States of America (2022) 119(4):e2115639118 https://doi.org/10.1073/pnas.2115639118

M. Weil, K. J. Hoff, M. Meißner, F. Schäfer, A. Söllinger, H. Wang, L. Hagenau, A. Kuß, T. Urich
Full genome sequence of a Methanomassilicoccales representative enriched from peat soil
Microbial Resource Announcements (2021) https://doi.org/10.1128/MRA.00443-21

L. Gabriel, K. J. Hoff, T. Bruna, M. Borodovsky, M.Stanke
TSEBRA: Transcript Selector for BRAKER
BMC Bioinformatics (2021) 22:566 https://doi.org/10.1186/s12859-021-04482-0. Preprint on [bioRxiv]

T. W. Wöhner, O. F. Emeriewen, A. H. J. Wittenberg, H. Schneiders, I. Vrijenhoek, J. Halász, K. Hrotkó, K. J. Hoff, L. Gabriel, J. Keilwagen, T. Berner, M. Schuster, A. Peil, J. Wünsche, S. Kropop, H. Flachowsky
The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads.
Genomics (2021) 113(6):4173-4183 https://doi.org/10.1016/j.ygeno.2021.11.002. Preprint on [bioRxiv]

M. Errbil, J. Keilwagen, K. J. Hoff, R. Steffen, J. Altmüller, J. Oettler, L. Schrader
Transposable elements and introgression introduce genetic variation in invasive ant Cardiocondyla obscurior
Molecular Ecology (2021) https://doi.org/10.1111/mec.16099

R. Harting, A. Nagel, K. Nesemann, A. M. Höfer, H. Kusch, C. E. Stanley, M. Stöckli, A. Kaever, K. J. Hoff, M. Stanke, A. J. deMello, M. Künzler, C. H. Haney, S. A. Braus-Stromeyer, G. H. Braus.
Pseudomonas strains induce transcriptional and morphological changes and reduce root colonization of Verticillium spp.
Frontiers in Microbiology (2021) https://doi.org/10.3389/fmicb.2021.652468.

B. Fouks, P. Brand, H. N. Nguyen, J. Herman, F. Camara, D. Ence, D. Hagen, K. J. Hoff, S. Nachtweide, L. Romoth, K. K. O. Walden, R. Guigo, M. Stanke, G. Narzisi, M. Yandell, H. M. Robertson, N. Koeniger, P. Chantawannakul, M. C. Schatz, K. C. Worley, G. E. Robinson, C. G. Elsik, O. Rueppell.
The genomic basis of evolutionary differentiation among honey bees.
Genome Research (2021) doi:10.1101/gr.272310.120.

R. Harting, J. Starke, H. Kusch, S. Pöggeler, I. Maurus, R. Schlüter, M. Landesfeind, I. Bulla, M. Nowrousian, R. de Jonge, G. Stahlhut, K. J. Hoff, K. P. Aßhauer, A. Thürmer, M. Stanke, R. Daniel, B. Morgenstern, B. P. H. J. Thomma, J. W. Kronstad, S. A. Braus-Stromeyer, G. H. Braus.
A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum
Molecular Plant Pathology (2021) mpp.13071. 

M. M. Sheffer, A. Hoppe, H. Krehenwinkel, G. Uhl, A. W. Kuss, L. Jensen, R. G. Gillespie, K. J. Hoff, S. Prost
Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation.
GigaScience (2021) 10(1):giaa148. Preprint on [bioRxiv]

T. Bruna, K. J. Hoff, A. Lomsadze, M. Stanke, M. Borodovsky
BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database.
NAR Genomics and Bioinformatics (2021) 3(1):Iqaa108. Preprint on [bioRxiv]

D. Ruiz-Ramos, L. Schiebelhut, K. J. Hoff, J. Wares and M. Dawson
An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars.
Molecular Ecology (2020) 29(6):1087-1102 https://doi.org/10.1111/mec.15386.

K. J. Hoff
MakeHub: Fully automated generation of UCSC Genome Browser Assembly Hubs
Genomics, Proteomics and Bioinformatics (2020) 17(5):546-549, 2020. Preprint on [bioRxiv]

I. Petersen, R. Schlüter, K. J. Hoff, V. Liebscher, G. Bange, K. Riedl, J. Pané-Farré
Non-invasive and label-free 3D visualization of proteins in bacterial cells.
Scientific Reports (2020) 10:125.

M. Stanke, W. Bruhn, F. Becker, K. J. Hoff
VARUS: sampling complementary RNA reads from the sequence read archive
BMC Bioinformatics (2019) 20:558. Preprint on [bioaRxiv]

H. Philippe, A. J. Poustka, M. Chiodin, K. J. Hoff, C. Dessimoz, B. Tomiczek, P. H. Schiffer, S. Müller, D. Domman, M. Horn, H. Kuhl, B. Timmermann, N. Satoh, T. Hikosaka-Katayama, H. Nakano, M. L. Rowe, M. R. Elphick, M. Thomas-Chollier, T. Hankeln, F. Mertes, A. Wallberg, J. P. Rast, R. R. Copley, P. Martinez, and M. J. Telford
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria 
Current Biology (2019) https://doi.org/10.1016/j.cub.2019.04.009

K. J. Hoff, S. Lange, A. Lomsadze, M. Borodovsky, M. Stanke
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Bioinformatics (2015) doi: 10.1093/bioinformatics/btv661 In February 2016, BioTechniques reports about BRAKER1.

B. M. Sadd, S.M. Barribeau, G. Bloch, D. C. de Graaf, P. Dearden, C. G. Elsik, J. Gadau, C. J. P. Grimmelikhuijzen, M. Hasselmann, J. D. Lozier, H. M. Robertson, G. Smagghe, E. Stolle, M. Van Vaerenbergh, R. M. Waterhouse, E. Bornberg-Bauer, S. Klasberg, A. K. Bennett, F. Camara, R. Guigo, K. Hoff, M. Mariotti, M. Munoz-Torres, T. Murphy, D. Santesmasses, G. V. Amdam, M. Beckers, M. Beye, M. Biewer, M. M. G. Bitondi, M. L. Blaxter, A. F. G. Bourke, M. J. F. Brown, S. D. Buechel, R. Cameron, K. Cappelle, J. C. Carolan, O. Christiaens, K. L. Ciborowski, D. F. Clarke, T. J. Colgan, D. H. Collins, A. G. Cridge, T. Dalmay, S. Dreier, L. du Plessis, E. Duncan, S. Erler, J. Evans, T. Falcon, F. C. P. Freitas, T. Fuchikawa, T. Gempe, K. Hartfelder, F. Hauser, S. Helbing, F. C. Humann, F. Irvine, L. S. Jermiin, C. E. Johson, R. M. Johnson, A. K. Jones, T. Kadowaki, J. H. Kidner, V. Koch, A. Köhler, F. B. Kraus, H. M. G. Lattorff, M. Leask, G. A. Lockett, E. B. Mallon, D. S. M. Antonio, M. Marxer, I. Meeus, R. F. A. Moritz, A. Nair, K. Näpflin, I. Nissen, J. Niu, J. G. Oakeshott, A. Osborne, M. Otte, D. G. Pinheiro, N. Rossie, O. Rueppell, C. G. Santos, R. Schmid-Hempel, B. D. Schmitt, C. Schulte, Z. L. P. Simoes, M. P. M. Soares, L. Swevers, E. C. Winnebeck, F. Wolschin, N. Yu, E. M. Zdobnov, P. K. Aqrawi, K. P. Blankenburg, M. Coyle, L. Francisco, A. G. Hernandez, M. Holder, M. E. Hudson, L. Jackson, J. Jayaseelan, V. Joshi, C. Kovar, S. L. Lee, R. Mata, T. Mathew, I. F. Newsham, R. Ngo, G. Okwuonu, C. Pham, L.-L. Pu, N. Saada, J. Santibanez, D. Simmons, R. Thomton, A. Venkat, K. K. O. Walden, Y.-Q. Wu, G. Debyser, B. Devreese, C. Asher, J. Blommaert, A. D. Chipman, L. Chittka, B. Fouks, J. Liu, M. P. O'Neill, S. Sumner, D. Puiu, J. Qu, S. L. Salzberg, S. E. Scherer, D. M. Muzny, S. Richards, G. E. Robinson, R. A. Gibbs, P. Schmid-Hempel, K. C. Worley
The genomes of two bumblebee species with primitive eusocial organization
Genome Biology (2015) 16:76

K. J. Hoff, M. Stanke
Current Methods for Automated Annotation of Protein-Coding Genes
Current Opinion in Insect Science (2015), doi:10.1016/j.cois.2015.02.008

E. Perea-Atienza, B. Gavilan, M. Chiodin, J.F. Abril, K.J. Hoff, A.J. Poustka, P. Martinez
The nervous system of Xenacoelomorpha: a genomic perspective
The Journal of Experimental Biology (2015) 218, 618-628 doi:10.1242/jeb.110379

C. G. Elsik, K.C. Worley, A. K. Bennett, M. Beye, F. Camara, C. P. Childers, D.C. Graaf, G. Debyser, J. Deng, B. Devreese, E. Elhaik, J. D. Evans, L. J. Foster, D. Graur, R. Guigo, HGSC production teams, K. J. Hoff, M. E. Holder, M. E. Hudson, G. J. Hunt, H. Jiang, V. Joshi, R. S. Khetani, P. Kosarev, C. L. Kovar, J. Ma, R. Maleszka, R. F. A. Moritz, M. C. Munoz-Torres, T. D. Murphy, D. M. Muzny, I. R. Newsham, J. T. Reese, H. M. Robertson, G. E. Robinson, O. Rueppell, V. Solovyev, M. Stanke, E. Stolle, J. M. Tsuruda, M. Van Vaerenbergh, R. M. Waterhouse, D. B. Weaver, C. W. Whitfield, Y. Wu, E. M. Zdobnov, L. Zhang, D. Zhu, R. A. Gibbs, and on behalf of the Honey Bee Genome Sequencing Consortium
Finding the missing honey bee genes: lessons learned from a genome upgrade
BMC Genomics 2014, doi:10.1186/1471-2164-15-86

V.-T. Tran, S.A. Braus-Stromeyer, H. Kusch, M. Reusche, A. Kaever, A. Kühn, O. Valerius, M. Landesfeind, K. Aßhauer, M. Tech, K. J. Hoff, T. Pena-Centeno, M. Stanke, V. Lipka and G.H. Braus
Verticillium transcription activator of adhesion Vta2 suppresses microscletoria formation and is required for systemic infection of plant roots
New Phytologist 2014, doi:10.111/nph.12671

K. J. Hoff, M. Stanke
WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes
Nucleic Acids Research, Web Server Issue 2013, doi:10.1093/nar/gkt418

K. K. Dasmahapatra, J. R. Walters, A. D. Briscoe, J. W. Davey, A. Whibley, N. J. Nadeau, A. V. Zimin, D. S. T. Hughes, L. C. Ferguson, S. H. Martin, C. Salazar, J. J. Lewis, S. Adler, S.-J. Ahn, D. A. Baker, S. W. Baxter, N. L. Chamberlain, R. Chauhan, B. A. Counterman, T. Dalmay, L. E. Gilbert, K. Gordon, D. G. Heckel, H. M. Hines, K. J. Hoff, P. W. H. Holland, E. Jacquin-Joly, F. M. Jiggins, R. T. Jones, D. D. Kapan, P. Kersey, G. Lamas, D. Lawson, D. Mapleson, L. S. Maroja, A. Martin, S. Moxon, W. J. Palmer, R. Papa, A. Papanicolaou, Y. Pauchet, D. A. Ray, N. Rosser, S. L. Salzberg, M. A. Supple, A. Surridge, A. Tenger-Trolander, H. Vogel, P. A. Wilkinson, D. Wilson, J. A. Yorke, F. Yuan, A. L. Balmuth, C. Eland, K. Gharbi, M. Thomson, R. A. Gibbs, Y. Han, J. C. Jayaseelan, C. Kovar, T. Mathew, D. M. Muzny, F. Ongeri, L.-L. Pu, J. Qu, R. L. Thornton, K. C. Worley, Y.-Q. Wu, M. Linares, M. L. Blaxter, R. H. ffrench-Constant, M. Joron, M. R. Kronforst, S. P. Mullen, R. D. Reed, S. E. Scherer, S. Richards, J. Mallet, W. Owen McMillan and C. D. Jiggins
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
Nature 2012, doi:10.1038/nature11041

K. J. Hoff
The effect of sequencing errors on metagenomic gene prediction
BMC Genomics 2009, 10:520

K. J. Hoff, T. Lingner, P. Meinicke, M. Tech
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research 2009, 37, W101-W105

K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke
Gene prediction in metagenomic fragments: a large scale machine learning approach
BMC Bioinformatics 2008, 9:217

K. J. Hoff, A. Lomsadze, M. Borodovsky and M. Stanke
Whole-Genome Annotation with BRAKER, 2019, Methods Mol Biol. 1962:65-95, DOI: 10.1007/978-1-4939-9173-0_5

K. J. Hoff and M. Stanke
Predicting Genes in Single Genomes with AUGUSTUS, 2018, Current Protocols in Bioinformatics, DOI: 10.1002/cpbi.57

K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke
Gene prediction in metagenomic fragments with Orphelia: a large scale machine learning, 2011, appeared in "Handbook of Molecular Microbial Ecology I: Metagenomic and Complementary Approaches" p. 359-367, DOI: 10.1002/9781118010518.ch41

T. Bruna, H. Li, J. Guhlin, D. Honsel, S. Herbold, M. Stanke, N. Nenasheva, M. Ebel, L. Gabriel and K. J. Hoff
Proteins Only: How Accurately Can We Annotate Large Genomes?
International Plant & Animal 31 Conference 2024, U.S.A.

N. Huang, T. Bruna and K. J. Hoff
Enhancing BRAKER3 for Eukaryotic Genome Annotation: Improved Transcript Selection with TSEBRA and a Step Towards Isoseq Integration
International Plant & Animal 31 Conference 2024, U.S.A.

L. Gabriel, K. J. Hoff, T. Bruna, A. Lomsadze, M. Borodovsky and M. Stanke
The BRAKER3 Genome Annotation Pipeline
International Plant & Animal XXIX Conference 2023, U.S.A.

K. J. Hoff
MakeHub: Creating Individual Assembly Hubs for Display with the UCSC Genome Browser
International Plant & Animal XXVIII Conference 2020, U.S.A.

K. J. Hoff, T. Bruna, A. Lomsadze, M. Stanke and M. Borodovsky
Fully Automated and Accurate Annotation of Genomes with BRAKER2
International Plant & Animal XXVIII Conference 2020, U.S.A.

M. Stanke and K. J. Hoff
Automatic Genome Annotation Looping over Species
International Plant & Animal XXVII Conference 2019, U.S.A.

T. Bruna, K. J. Hoff, A. Lomsadze, M. Stanke and M. Borodovsky
BRAKER2: A Pipeline Integrating Data on Genomic, RNA and Protein Sequences into Inference of Plant and Animal Genome Annotation
International Plant & Animal XXVII Conference 2019, U.S.A.,poster (pdf)

K. J. Hoff, A. Lomsadze, M. Stanke and M. Borodovsky
BRAKER2: Incorporating Protein Homology Information into Gene Prediction with AUGUSTUS and GeneMark-EP
International Plant & Animal XVI Conference 2018, U.S.A.

L. W. Bruhn, K. J. Hoff and M. Stanke
VARUS: Drawing Diverse Samples from RNA-Seq Libraries
International Plant & Animal XVI Conference 2018, U.S.A.

E. Perea-Atienza, B. Gavilàn, J. F. Abril, K.J. Hoff, A.J. Poustka, P. Martinéz
The nervous system of Xenocoelomorpha: a tale of progressive cephalization
Euro Evo Devo 2014, Austria

K. J. Hoff, T. Pena Centeno, Sebastian Adler and M. Stanke
Predicting Genes with AUGUSTUS and RNA-Seq Data
International Plant & Animal XXII Conference 2014, U.S.A

K. J. Hoff, Tonatiuh Pena Centeno, Sebastian Adler and Mario Stanke
Incorporating RNA-Seq data into AUGUSTUS: Gene prediction accuracy derived from three mapping tools
Meeting on Advances and Challenges of RNA-Seq Analysis 2012, Germany

K. J. Hoff and M. Stanke
TrainAUGUSTUS -  A Webserver Application for Parameter Training and Gene Prediction in Eukaryotes.
International Plant & Animal XX Conference 2012, U.S.A

C. Carmeli, K. J. Hoff, S. v.d. Heyde, C. Bender, F. Henjes, V. Szabo, H. Mannsperger, D. Arlt, S. Wiemann, A. Schneeweiss, M. Hasmann, U. Korf, T. Beissbarth, J. Timmer
Multivariate soft modeling to evaluate the quality and information content of protein array data
MedSys Status Seminar 2010, Germany

K. J. Hoff, F. Schreiber, M. Tech, P. Meinicke
The effect of sequencing errors on metagenomic gene prediction
ISMB/ECCB 2009, Sweden

K. J. Hoff, M. Tech, P. Meinicke
Predicting genes on metagenomic pyrosequencing reads with machine learning techniques
GCB 2008, Germany

K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke
Gene prediction in metagenomic DNA fragments
Horizons in Molecular Biology 2008, Germany

K. J. Hoff, M. Tech, P. Meinicke
Gene prediction in metagenomic DNA fragments with machine learning techniques
Genomes 2008, France

K. J. Hoff, M. Tech, P. Meinicke
Predicting genes in metagenomic DNA fragments with high specificity using machine learning techniques
ECCB 2008, Italy

K. J. Hoff, M. Tech, P. Meinicke
Predicting genes in short metagenomic sequencing reads with high specificity
Metagenomics 2008, U.S.A.

Annotation of Protein Coding Genes, 2024 Workshop on Genomics, Cesky Krumlov, Czech Republic, 2024. slides

Proteins Only: How Accurately Can We Annotate Large Genomes? International Plant & Animal Genome 31, U.S.A., 2024. slides about GALBA

Enhancing BRAKER3 for Eukaryotic Genome Annotation: Improved Transcript Selection with TSEBRA and a Step Towards Isoseq Integration, International Plant & Animal Genome 31, 2024. slides about BRAKER3

Genome Annotation with BRAKER, GALBA, and TSEBRA, 2023 Workshop on Genomics, Cesky Krumlov, Czech Republic, 2023.

Fully Automated Genome Annotation - a Game Changer for Genomics, 2021, University of Duisburg, Duisburg.

Fully Automated Genome Annotation and Beyond, 2021, University of Potsdam/Max Planck Institute of Molecular Plant Physiology, Online.

Introduction to Horticulture & Connection to Genome Annotation, 2021,  University of Potsdam/Max Planck Institute of Molecular Plant Physiology, Online.

Fully Automated and Accurate Annotation of Eukaryotic Genomes with BRAKER2, International Plant & Animal Genome XXVIII, U.S.A., 2020. Also see poster and slides about BRAKER2.

MakeHub: Creating Individual Assembly Hubs for Display with the UCSC Genome Browser, International Plant & Animal Genome XXVIII, U.S.A., 2020. Also see poster and slides about MakeHub.

Fully Automated Genome Annotation and Beyond, 2019, University of Wageningen, Wageningen (Netherlands).

Automating Highly Accurate Gene Prediction, 2018, University of Hohenheim, Hohenheim.

Identifizierung von Genen in genomischen Sequenzen, 2018, University of Hohenheim, Hohenheim.

BRAKER2: Incorporating Protein Homology Information into Gene Prediction with GeneMark-EP and AUGUSTUS, International Plant & Animal Genome XXVI, U.S.A., 2018. Also see poster and slides about BRAKER2.

High Quality and Fully Automated Gene Prediction, 2017, University of Bergen, Bergen (Norway).

Pairwise sequence alignment, 2017, University of Bergen, Bergen (Norway).

BRAKER1: Unsupervised RNA-Seq-based Genome Annotation with GeneMark-ET and AUGUSTUS, International Plant & Animal Genome XXIII, U.S.A, 2015. Also see poster about BRAKER1.

Integrating RNA-Seq Data with AUGUSTUS, 2012, Center for Biotechnology, Bielefeld

Integrating RNA-Seq Data with AUGUSTUS, 2012, Memorial Sloan-Kettering Cancer Center, New York

Basic Statistics, 2D-DIGE 3rd International Workshop, 2010, Bochum

Basic Statistics, 4th European Summer School "Proteomic Basics - High-Throughput Data Analysis and Statistics", 2010, Brixen

Gene prediction in metagenomic sequencing reads, Department für Geo- und Umweltwissenschaften,
Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München, 2009, München

Orphelia: a tool for predicting genes in metagenomic sequencing reads, sIT 2009, Göttingen

Habilitation Thesis (University of Greifswald, Germany, 2020):
Improving and Automating the Prediction of Protein Coding Genes in Eukaryotic Genomes

PhD Thesis (University of Göttingen, Germany, 2009):
Gene prediction in metagenomic sequencing reads

Bachelor Thesis (University of Hannover, Germany, 2005):
R-Handbook for Biostatistics
(English version of thesis, German version of thesis, data_sets.zip)

I am currently looking for students who would like to do their thesis on the following topics:

• Deep Learning for annotating genes in poorly represented clades
• Developing a read-centric prediction method for identification of resistance genes (in metagenomic data) (software development, collaboration with Prof. Dr. Katharina Schaufler @HIOH in Greifswald)

In general, if you decide to do your thesis project in my team, you will usually learn about open problems in bioinformatics (or related fields), software development, using HPC systems, and handling large data. Please contact me in case you are interested in doing a Bachelor, Master or Diploma thesis in our group. Prof. Dr. Mario Stanke also offers amazing topics.

Other groups that might offer thesis topics in the area of bioinformatics at University of Greifswald:

• Lars Kaderali's group

• Tim Kaufmann "Phycosphere community assembly in Conticriba weissflogii cultures in response to inculum source and lig (since 2024) Universität Greifswald (Master thesis)
• Julia Thu Anh Nguyen "Systematic comparison of fully automated pipelines for MAG reconstruction - a case study in baltic sea seagrass microbiomes (2024) Universität Greifswald (Bachelor thesis)
• Clara Pitzschel "Training a deep learning gene finder for diatoms" (2024) Universität Greifswald (Bachelor thesis)
• Simon Brandt "Assessment of consistency and improvement of structural genome annotation with comparative methods" (2024) Universität Greifswald (Master thesis)
• Natalia Nenasheva "Gene prediction in the eukaryotic proportion of metagenomes" (since 2022) Universität Greifswald (PhD thesis)
• Thomas Rohde "Phylogenetic and genomic analysis of globally disseminated antibiotic-resistant Klebsiella pneumoniae sequence type 395 (2022) Universität Greifswald (Master thesis)
• Hannah Thierfeldt "Fully automated genome annotation with long read RNA-Seq data" (2021) Universität Greifswald (Bachelor thesis)
• Larissa Busch "Assembly and annotation of the wasp spider endosymbiont genome" (2020) Universität Greifswald (Bachelor thesis)
• Anica Hoppe "Assembly and annotation of the genome of Argiope bruennichi" (2020) Universität Greifswald (Master thesis)
• Jasmin Franke "How quorum sending mutants influence the proteome of Burkholderia pseudomallei" (2020) Universität Greifswald (Master thesis)
• Jacob Schneider "Using machine learning techniques for scoring predicted gene models according to extrinsic evidence." (2020) Universität Greifswald (Bachelor thesis)
• Walther Meißner "Assembly and annotation of a prokaryotic genome from enrichment culture" (2019) Universität Greifswald (Bachelor thesis)
• Leonie Lorenz "A pipeline improving prokaryotic genome annotation with peptide data from MS/MS experiments" (2019) Universität Greifswald (Bachelor thesis)
• Simone Lange "RNA-Seq-basierte strukturelle Genomannotation basierend auf unüberwachtem Training" (2015) Universität Greifswald (Master thesis)
• Kristina Wicke "The Shapley Value and the Fair Proportion Index as measures of Biodiversity - Analysis, Comparison and Computation" (2014) Universität Greifswald (Bachelor thesis)
• Annika Frankenberger "Entwicklung einer App mit dem Android SDK zur Auswahl von Musiktiteln basierend auf Messungen einer Beschleunigungssensors" (2013) Universität Greifswald (Bachelor thesis)
• Maria Hartmann "Die Identifizierung von untranslatierten Bereichen von Transkripten mit Hilfe von RNA-Seq Daten" (2013) Universität Greifswald (Bachelor thesis)
• Kristina Plate "Bioinformatische und experimentelle Analyse von Promotoren in Streptococcus pneumoniae" (2011) Universität Greifswald (Bachelor thesis)
• Christian Müller "Evaluation zum Einfluss einer vorgeschalteten Genvorhersage bei der Detektion von Proteindomänen in der Metagenomik" (2011) Georg-August-Universität Göttingen (Bachelor thesis)