PD Dr. Katharina Hoff

Contact

Mail address:

Institut für Mathematik und Informatik
Walther-Rathenau-Str. 47
17489 Greifswald

Office:Felix-Hausdorff-Str. 8, Room 0.62 (C_FunGene).

Phone: +49 3834 420 4624

katharina.hoff@uni-greifswald.de

Profile on ResearchGate

Profile on GoogleScholar

see Bioinformatics Group

For young women in science: University of Greifwald has excellent mentoring programs.

Enrolling as an undergraduate in our study programs at MathInf:Pre-course for beginners is open for registration, now! (course is in German)

Consultation Hours

Feel free to call me any time between 9:00 and 17:00 on weekdays, do not supress caller ID, I will call back.

Software/Web Services

GALBA - a tool for unsupervised fully automated genome annotation with AUGUSTUS and miniprot: https://github.com/Gaius-Augustus/GALBA

TSEBRA - Transcript Selector for BRAKER: https://github.com/Gaius-Augustus/TSEBRA

GUSHR - Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation: https://github.com/Gaius-Augustus/GUSHR

VARUS - Drawing Diverse Samples from RNA-Seq Libraries: https://github.com/Gaius-Augustus/VARUS

MakeHub - a tool for fully automated generation of assembly hubs for omics data visualization with the UCSC Genome Browser: https://github.com/Gaius-Augustus/MakeHub

BRAKER - a tool for unsupervised RNA-seq- or protein-based genome annotation with GeneMark and AUGUSTUS: https://github.com/Gaius-Augustus/BRAKER

webAUGUSTUS - a web service for eukaryotic gene prediction and parameter training: http://bioinf.uni-greifswald.de/webaugustus

AUGUSTUS - a gene prediction tool for pro- and eukaryotes (actively contributing to scripts & auxprogs): https://github.com/Gaius-Augustus/Augustus

Orphelia - a tool for metagenomic gene prediction (at University of Göttingen): http://orphelia.gobics.de/

Reconstruct-Parser - a parser for Reconstruct XML files of electron microscopy images with marked contours: https://github.com/KatharinaHoff/Reconstruct-Parser

Teaching

SS 2024

SS 2024

Diese Inhalte sind noch nicht angepasst, Aktualisierung folgt.

Bioinformatisches Praktikum (Vorlesung/ÜbungMoodle-Course)

Bioinformatisches Praktikum für Studierende der Humanbiologie (Moodle-Course)

Statistik I Vorlesung (Vorlesung/ÜbungMoodle-Course)

Project: Data Competency

Project: Data Competency

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

In the past

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.

Subjects of interest

  • Eukaryotic and prokaryotic gene prediction
  • Metagenomics
  • Genome annotation
  • Sequence analysis
  • Workflow automation
  • Analysis of biological/medical data
Short CV
2022 Habilitation in Bioinformatics and venia legendi for Bioinformatics at University of Greifswald. Colleagues from abroad have been asking me what the "PD" means. It stands for "Privatdozentin" and is associated with the completed habilitation. According to dictionaries, it translates to "assistant professor" or "associate professor" - but I am not employed as a professor..
since 2020 Member of the Earth Biogenome Project Standards Committee on Genome Annotation
2019-2021 Mentee in mentoring program for postdocs and assistant professors at University of Greifswald
since 2013 Open-ended scientific staff contract at Universität Greifswald
2010-2013 Postdoc at Universität Greifswald, research focus: improving genome annotation
since 2010 Freelance consultant for bioinformatics and biostatistics, Greifswald (secondary job)
2010 Postdoc at Georg August Universität Göttingen, project: genome annotation of Verticillium longisporum (6 months, working from Greifswald)
2010 Postdoc at Universitätsklinikum Göttingen, research focus: modeling drug resistance in breast cancer cell lines (6 months)
2009-2010 Management Assistant at BitConf - Benedikt Frank & Burkhard Heisen GbR, Göttingen (secondary employment)
2005-2009 M.Sc./Ph.D. program Molecular Biology, Max Planck Research School and Georg August Universität Göttingen, thesis: Gene Prediction in Metagenomic Sequencing Reads
2004-2005 Swedish University of Agricultural Sciences, Alnarp, Sweden (13 months), ERASMUS studies and 6-months internship in lipid research group
2003 2-months Internship at Institute for Pharmacognosy, Department for Pharmacy, Semmelweis University Budapest, Hungary
2002-2005 B.Sc. program Plant Biotechnology, Leibniz Universität Hannover, thesis: R-Handbook for students of Horticulture and Plant Biotechnology
Stipends/Grants
2023-2026 Project AI-Biome within ArtIFARM, an initiative in WIR! Wandel durch Innovation in der Region: Subproject 1 Development of AI-based software for investigation of life stock
2022-2024 Subproject within German Research Association funded Research Group Proteogenomics of Marine Polysaccharide Utilization (POMPU) - SP3: Mechanisms of polysaccharide degradation in particle-associated microbial communities
2019-2023 Data Competency (Hochschulpaktmittel) - Advancing students in handling and analysing big data
2011-2013 Own Position (German Research Foundation "Sachbeihilfe") - Reliable structural genome annotation of Archaea
2008 Göttingen Graduate School for Neurosciences and Molecular Biosciences travel grant
2006-2008 Georg Christoph Lichtenberg PhD stipend (living costs)
2005-2006 Max-Planck-Research-School MSc stipend (living costs)
2005 Stipend by the Swedish University of Agricultural Sciences Alnarp (partial living costs)
2004- 2005 ERASMUS stipend (partial living costs and travel grant)
2004-2005 Stiftung der Deutschen Wirtschaft (undegraduate book stipend)
2003-2009 e-fellows.net stipend (online stipend)

Publications

Science for the Public

Science for the Public

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

Preprints only

Preprints only

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

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
ResearchSquare (2023) https://doi.org/10.21203/rs.3.rs-3777552/v1

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
bioRxiv (2023) https://doi.org/10.1101/2023.06.10.544449

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
The slowly evolving genome of the xenacoelomorph worm Xenoturbella bocki
bioRxiv (2022) https://doi.org/10.1101/2022.06.24.497508

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

Peer reviewed papers

Peer reviewed papers

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

Book chapters

Book chapters

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

Conference posters

Conference posters

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.

Invited Talks

Invited Talks

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

Theses

Theses

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 thesisGerman version of thesis, data_sets.zip)

Available thesis topics

Currently available topics

Currently available topics

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

  • De novo assembly and annotation of two diatom genomes (data analysis, collaboration with Prof. Dr. Thomas schweder @PharmaceuticalBiotechnology in Greifswald)
  • Improving the quality of plasmidfinder analysis (software development, collaboration with Prof. Dr. Katharina Schaufler @HIOH in Greifswald)
  • 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:

Current and past thesis projects under my (co-)supervision

Current and past thesis projects under my (co-)supervision

  • Julia Thu Anh Nguyen "Systematic comparison of fully automated pipelines for MAG reconstruction - a case study in baltic sea seagrass microbiomes (since 2023) Universität Greifswald (Bachelor thesis)
  • Clara Pitzschel "Training a deep learning gene finder for diatoms" (since 2024) Universität Greifswald (Bachelor thesis)
  • Simon Brandt "Assessment of consistency and improvement of structural genome annotation with comparative methods" (since 2023) 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)

Referee Services for

  • PLoS ONE
  • BMC Bioinformatics
  • Nucleic Acids Research
  • Algorithms for Molecular Biology
  • BMC Genomics
  • Molecular Ecology Resources
  • Cell
  • Nature Communications
  • Genetics and Molecular Biology
  • Applications in Plant Sciences

Acknowledgements

We thank the University Computer Center, in particular High Performance Computing, for outstanding support and service.