Dr. Katharina Hoff

Contact

Dr. Katharina Hoff

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

Office: Franz-Mehring-Str. 48 (first floor [1.OG], first door to the right)

Phone +49 3834 420 4624
katharina.hoff(at)uni-greifswald(dot)de

see professor for Bioinformatics

Subjects of interest

  • Eukaryotic and prokaryotic gene prediction
  • Metagenomics
  • Genome annotation
Short CV
2013-now Open-ended scientific staff contract at Universität Greifswald
2010-2013 Postdoc at Universität Greifswald, research focus: improvement of pro- and eukaryotic gene prediction, integration of RNA-Seq data into gene prediction, genome annotation
2010-now 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
2011-2013 Eigene Stelle (DFG-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- 005 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)

Consultation Hours

Wednesday 9-10 on appointment, and at all other times when I happen to be in my office.

Publications

Peer reviewed papers

Peer reviewed papers

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, 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

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

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

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

PhD Thesis (University of Göttingen, Germany, 2009):
Gene prediction in metagenomic sequencing readshttp://gobics.de/peter

Bachelor Thesis (University of Hannover, Germany, 2005):
R-Handbook for Biostatistics
(English version of thesisGerman version of thesis)

Software/Web Services

BRAKER1 - a tool for unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS

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

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

Teaching

WS 2015/16

WS 2015/16

parental leave

SS 2015

SS 2015

parental leave

SS 2015
In the past

At University of Greifswald, I participated in teaching the M.Sc. Biomathematics Module "Bioinformatics" by covering the topic "Microarray Analysis with R".

I gave the following courses at other institutions:

  • 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.

Available thesis topics

Please contact me in case you are interested in doing a Bachelor, Master or Diploma thesis in our group.

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

  • Simone Lange "RNA-Seq-basierte strukturelle Genomannotation basierend auf unüberwachtem Training" (2015) Ernst-Moritz-Arndt Universität Greifswald (Master thesis)
  • Kristina Wicke "The Shapley Value and the Fair Proportion Index as measures of Biodiversity - Analysis, Comparison and Computation" (2014) Ernst-Moritz-Arndt Universität Greifswald (Bachelor thesis)
  • Annika Frankenberger "Entwicklung einer App mit dem Android SDK zur Auswahl von Musiktiteln basierend auf Messungen einer Beschleunigungssensors" (2013) Ernst-Moritz-Arndt Universität Greifswald (Bachelor thesis)
  • Maria Hartmann "Die Identifizierung von untranslatierten Bereichen von Transkripten mit Hilfe von RNA-Seq Daten" (2013) Ernst-Moritz-Arndt Universität Greifswald (Bachelor thesis)
  • Kristina Plate "Bioinformatische und experimentelle Analyse von Promotoren in Streptococcus pneumoniae" (2011) Ernst-Moritz-Arndt 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