Publications


This page lists publications of our group since 2011. Please refer to the websites of individual group members for publications before 2011.

2018

  • K.J. Hoff and M. Stanke
    Predicting Genes in Single Genomes with AUGUSTUS
    Current Protocols in Bioinformatics, doi:10.1002/cpbi.57
  • Note of correction
    On page 42, two references are missing for GEMOMA:
    • Keilwagen, J., Wenk, M., Erickson, J. L., Schattat, M. H., Grau, J., & Hartung, F. (2016). Using intron position conservation for homology-based gene prediction. Nucleic acids research, 44(9), e89-e89.
    • Keilwagen, J., Hartung, F., Paulini, M., Twardziok, S. O., & Grau, J. (2018). Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC bioinformatics, 19(1), 189.
  • S. König, L. Romoth, M. Stanke
    Comparative Genome Annotation
    In: Setubal J., Stoye J., Stadler P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY, https://doi.org/10.1007/978-1-4939-7463-4_6
  • N. Nath, J. Esche, J. Müller, L.R. Jensen, M. Port, M. Stanke, L. Kaderali, H. Scherthan, A.W. Kuss
    Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva Fibroblasts
    Health Physics, doi: 10.1097/HP.0000000000000880
  • I.T. Fiddes, J. Armstrong, M. Diekhans, S. Nachtweide, Z. N. Kronenberg, J. G. Underwood, D. Gordon, D. Earl, T. Keane, E.E. Eichler, D. Haussler, M. Stanke, B. Paten
    Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
    Genome Research, doi: 10.1101/gr.233460.117
  • D. Thybert, M. Roller, F. C. P. Navarro, I. Fiddes, I. Streeter, C. Feig, D. Martin-Galvez, M. Kolmogorov, V. Janoušek, W. Akanni, B. Aken, S. Aldridge, V. Chakrapani, W. Chow, L. Clarke, C. Cummins, A. Doran, M. Dunn, L. Goodstadt, K. Howe, M. Howell, A.-A. Josselin, R. C. Karn, C. M. Laukaitis, L. Jingtao, F. Martin, M. Muffato, S. Nachtweide, M. A. Quail, C. Sisu, M. Stanke, K. Stefflova, C. Van Oosterhout, F. Veyrunes, B. Ward, F. Yang, G. Yazdanifar, A. Zadissa, D. J. Adams, A. Brazma, M. Gerstein, B. Paten, S. Pham, T. M. Keane, D. T. Odom, P. Flicek
    Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    Genome Research, doi:10.1101/gr.234096.117

2017

  • E. E. Schwager, P. P. Sharma, T. Clarke, D. J. Leite, T. Wierschin, M. Pechmann, Y. Akiyama-Oda, L. Esposito, J. Bechsgaard, T. Bilde, A. D. Buffry, H. Chao, H. Dinh, H. Doddapaneni, S. Dugan, C. Eibner, C. G. Extavour, P. Funch, J. Garb, L. Gonzalez, V. L. Gonzalez, S. Griffiths-Jones, Y. Han, C. Hayashi, M. Hilbrant, D. S. T. Hughes, R. Janssen, S. L. Lee, I. Maeso, S. C. Murali, D. M. Muzny, R. Nunes da Fonseca, C. L. B. Paese, J. Qu, M. Ronshaugen, C. Schomburg, A. Schoenauer, A. Stollewerk, M. Torres-Oliva, N. Turetzek, B. Vanthournout, J. H. Werren, C. Wolff, K. C. Worley, G. Bucher, R. A. Gibbs, J. Coddington, H. Oda, M. Stanke, N. A. Ayoub, N.-M. Prpic, J.-F. Flot, N. Posnien, S. Richards, A. P. McGregor
    The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
    BMC Biology, 15:62, DOI 10.1186/s12915-017-0399-x
  • S. Xu, T. Brockmöller, A. Navarro-Quezada, H. Kuhl, K. Gase, Z. Ling, W. Zhou, C. Kreitzer, M. Stanke, H. Tang, E. Lyons, P. Pandey, S. P. Pandey, B. Timmermann, E. Gaquerel, I. T. Baldwin
    Wild tobacco genomes reveal the evolution of nicotine biosynthesis
    PNAS, doi:10.1073/pnas.1700073114
  • B. Cai, B. Li, N. Kiga, J. Thusberg, T. Bergquist, Y.-C. Chen, N. Niknafs, H. Carter, C. Tokheim, V. Beleva-Guthrie, C. Douville, R. Bhattacharya, H. T. Grace Yeo, J. Fan, S. Sengupta, D. Kim, M. Cline, T. Turner, M. Diekhans, J. Zaucha, L. R. Pal, C. Cao, C.-H. Yu, Y. Yin, M. Carraro, M. Giollo, C. Ferrari, E. Leonardi, S. C. E. Tosatto, J. Bobe, M. Ball, R. Hoskins, S. Repo, G. Church, S. E. Brenner, J. Moult, J. Gough, M. Stanke, R. Karchin, S. D. Mooney
    Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges
    Human Mutation. doi:10.1002/humu.23265

2016

2015

  • K.J. Hoff and M. Stanke
    Current methods for automated annotation of protein-coding genes
    Current Opinion in Insect Science, https://doi.org/10.1016/j.cois.2015.02.008
  • T. Wierschin, K. Wang, M. Welter, S. Waack, M. Stanke
    Combining features in a graphical model to predict protein binding sites
    Proteins: Structure, Function, and Bioinformatics, https://doi.org/10.1002/prot.24775
  • J. Ulrich, U. Majumdar, C. Schmitt-Engel, J. Schwirz, D. Schultheis, N. Ströhlein, N. Troelenberg, D. Grossmann, T. Richter, J. Dönitz, L. Gerischer, G. Leboulle, A. Vilcinskas, M. Stanke, G. Bucher
    Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target
    BMC Genomics, https://doi.org/10.1186/s12864-015-1880-y
  • C. Schmitt-Engel, D. Schultheis, J. Schwirz, N. Ströhlein, N. Troelenberg, U. Majumdar, D. Grossmann, T. Richter, M. Tech, J. Dönitz, L. Gerischer, M. Theis, I. Schild, J. Trauner, N.D.B. Koniszewski, E. Köster, S. Kittelmann, Y. Hu, S. Lehmann, J. Siemanowski, J. Ulrich, K.A. Panfilio, R. Schröder, B. Morgenstern, M. Stanke, F. Buchhholz, M. Frasch, S. Roth, E.A. Wimmer, M. Schoppmeier, M. Klingler, G. Bucher
    The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology
    Nature Communications, doi: 10.1038/ncomms8822
  • 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 this publication.
  • 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, doi:10.1186/s13059-015-0623-3

2014

  • S. Dippel, G. Oberhofer, J. Kahnt, L. Gerischer, L. Opitz, J. Schachtner, M. Stanke, S. Schütz, E.A. Wimmer, and S. Angeli
    Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions
    BMC Genomics, 15(1):1141
  • I.K. Blaby, C.E. Blaby-Haas, N. Tourasse, E.F.Y. Hom, D. Lopez, M. Aksoy, A. Grossman, J. Umen, S. Dutcher, M. Porter, S. King, G.B. Witman, M. Stanke, E.H. Harris, D. Goodstein, J. Grimwood, J. Schmutz, O. Vallon, S.S. Merchant, and S. Prochnik
    The Chlamydomonas genome project: a decade on
    Trends in Plant Science, 19(10)
  • Z. Dong, K. Wang, T.K.L. Dang, M. Gültas, M. Welter, T. Wierschin, M. Stanke, S. Waack
    CRF-based models of protein surfaces improve protein-protein interaction site predictions
    BMC Bioinformatics, 15:277
  • 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. Hoff, T. Pena-Centeno, M. Stanke, V. Lipka, G. H. Braus (2014)
    Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots
    New Phytologist, doi:10.1111/nph.12671
  • S. Van der Auwera, I. Bulla, M. Ziller, A. Pohlmann, T. Harder, M.Stanke (2014)
    ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs
    PLoS One, 9(1):e84558

2013

  • K. J. Hoff, M. Stanke (2013)
    WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes
    Nucleic Acids Res, Web Server Issue 2013, doi: 10.1093/nar/gkt418
  • G. Schönknecht, W. H. Chen, C. M. Ternes, G. G. Barbier, R. P. Shrestha, M. Stanke, A. Bräutigam, B. J. Baker, J. F. Banfield, R. M. Garavito, K. Carr, C. Wilkerson, S. A. Rensing, D. Gagneul, N. E. Dickenson, C. Oesterhelt, M. J. Lercher, A. P. Weber (2013)
    Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote
    Science, Vol. 339 no. 6124 pp. 1207-1210

2012

  • F. Martin, L. Bovet, A. Cordier, M. Stanke, I. Gunduz, M. Peitsch and N. Ivanov (2012)
    Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties
    BMC Genomics, 13:674
  • G. Sablok, A. Sánchez-Paz, X. M. Wu, I. Bulla (2012)
    Genome dynamics in three different geo-graphical isolates of white spot syndrome virus (WSSV) genome
    Archives of Virology, 157(12), 2357-2362
  • A.-K. Schultz, I. Bulla, M. Abdou-Chekaraou, E. Gordien, B. Morgenstern, F. Zoulim, P. Deny and M. Stanke (2012)
    jpHMM: Recombination analysis in viruses with circular genomes such as the hepatitis B virus.
    Nucleic Acids Res, Web Server Issue 2012, 40(W1):W193-W198.
  • 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, C. D. Jiggins (2012)
    Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
    Nature, doi:10.1038/nature11041
  • I. Bulla, A.-K. Schultz, P. Meinicke (2012)
    Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 subtypes through Linear Discriminant Learning.
    Statistical Applications in Genetics and Molecular Biology, 11(1)

2011

  • R. Buckdahn, I. Bulla, J. Ma (2011)
    Pathwise Taylor Expansions for Itō Random Fields
    Mathematical Control and Related Fields , 1(4), 437-468
  • J. Bulla, S. Mergner, I. Bulla, A. Sesboüé, C. Chesneau (2011)
    Markov-switching Asset Allocation: Do Profitable Strategies Exist?
    Journal of Asset Management, 12(5), 310-321
  • F. Raymond, S. Boisvert, G. Roy, J. F. Ritt, D. Légaré, A. Isnard, M. Stanke, M. Olivier, M. J. Tremblay, B. Papadopoulou, M. Ouellette, J. Corbeil (2011)
    Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species.
    Nucl. Acids Res., 1-17, doi:10.1093/nar/gkr834
  • K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2011)
    Gene prediction in metagenomic fragments with Orphelia: a large scale machine learning, appeared in "Handbook of Molecular Microbial Ecology I: Metagenomic and Complementary Approaches" p. 359-367, DOI: 10.1002/9781118010518.ch41
  • T. Unterthiner, A.-K. Schultz, J. Bulla, B. Morgenstern, M. Stanke and I. Bulla (2011)
    Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.
    BMC Bioinformatics, 12:93
  • M. Specht, M. Stanke, M. Terashima, B. Naumann-Busch, I. Hanßen, R. Höhner, E.F.Y. Hom, C. Liang, M. Hippler (2011)
    Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome.
    Proteomics, 11(9)1814-1823
  • O. Keller, M. Kollmar, M. Stanke, S. Waack (2011)
    A novel hybrid gene prediction method employing protein multiple sequence alignments.
    Bioinformatics, doi: 10.1093/bioinformatics/btr010