Publications

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

2024

  • F. Becker, M. Stanke
    learnMSA2: deep protein multiple alignments with large language and hidden Markov models
    Bioinformatics 40(Issue Supplement_2):ii79-ii86, https://doi.org/10.1093/bioinformatics/btae381
  • 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, 15, https://doi.org/10.3389/fpls.2024.1437132
  • 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
  • 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, https://doi.org/10.7554/eLife.94948
  • S. Jain, C. Bakolitsa, E. B. Steven, P. Radiovojac, (...), M. Stanke, (...), J. M. Zook
    Critical assessment of genome interpretation consortium. CAGI, the critical assessment of genome interpretation, establishes progress and pprospects for computational genetic variant interpretation methods
    Genome Biology, doi:10.1186/s13059-023-03113-6
  • S. Nachtweide, L. Romoth, M. Stanke
    Comparative Genome Annotation
    Comparative Genomics, Methods and Protocols, doi:10.1007/978-1-0716-3838-5_7
  • 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, doi:10.1101/gr.278090.123.
  • 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, fiae037, doi: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, 31:26, doi:10.1186/s12929-024-01014-9.
  • T. Jung, I. Milenković, Y. Balci, J. Janoušek, T. Kudláček, Z.Á. Nagy, B. Baharuddin, J. Bakonyi, K.D. Broders, S.O. Cacciola, T.-T. Chang, N.M. Chi, T. Corcobado, A. Cravador, B. Đorđević, A. Durán, M. Ferreira, C.-H. Fu, L. Garcia, A. Hieno, H.-H. Ho, C. Hong, M. Junaid, K. Kageyama, T. Kuswinanti, C. Maia, T. Májek, H. Masuya, G. Magnano di San Lio, B. Mendieta-Araica, N. Nasri, L.S.S. Oliveira, A. Pane, A. Pérez-Sierra, A. Rosmana, E. Sanfuentes von Stowasser, B. Scanu, R. Singh, Z. Stanivuković, M. Tarigan, P.Q. Thu, Z. Tomić, M. Tomšovský, S. Uematsu, J.F. Webber, H.-C. Zeng, F.-C. Zheng, C.M. Brasier, M. Horta Jung
    Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity
    Studies in Mycology, 107:251-388, doi:10.3114/sim.2024.107.04.
  • 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, esad054, doi:10.1093/jhered/esad054

2023

  • 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, 14, doi:10.3389/fpls.2023.1284478.
  • T. Bruna, 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, 24:327, doi:10.1186/s12859-023-05449-z
  • 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, 30:52, doi:10.1186/s12929-023-00947-x
  • 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, 15:9, doi:10.1186/s13073-023-01159-6
  • M. Ebel, M. Domin, N. Neumann, C.O. Schmidt, M. Lotze, M. Stanke
    Classifying sex with volume-matched brain MRI
    Neuroimage: Reports, 3(3):100181, doi:10.1016/j.ynirp.2023.100181

2022

2021

  • L. Gabriel, K. J. Hoff, T. Bruna, M. Borodovsky, M.Stanke.
    TSEBRA: Transcript Selector for BRAKER
    BMC Bioinformatics 22:566, doi:10.1186/s12859-021-04482-0, preprint on biorXiv: https://doi.org/10.1101/2021.06.07.447316
  • 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, doi:10.1128/MRA.00443-21
  • T. W. Wöhner, O. F. Emeriewen, A. H. J. Wittenberg, H. Schneiders, I. Vrijenhoek, J. Halasz, K. Hrotko, 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, doi:10.1016/j.ygeno.2021.11.002
  • A. K. Schütz, V. Schöler, E. T. Krause, M. Fischer, T. Müller, C. M. Freuling, F. J. Conraths, M. Stanke, T. Homeier-Bachmann, H. H. K. Lentz.
    Application of YOLOv4 for Detection and Motion Monitoring of Red Foxes
    Animals, 11(6)1723, doi: 10.3390/ani11061723
  • M. Errbil, J. Keilwagen, K. J. Hoff, R. Steffen, J. Altmüller, J. Oettler, L. Schrader.
    Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior
    Molecular Ecology, doi: 10.1111/mec.16099
  • R. Harting, A. Nagel, K. Nesemann, A. M. Höfer, E. Bastakis, 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, doi: 30.3389/fmicb.2021.652468
  • 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, mpp.13071, doi: 10.1111/mpp.13071
  • 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, doi: 10.1101/gr.272310.120
  • 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
    Giga Science, 10(1):giaa148 , preprint on biorXive: https://doi.org/10.1101/2020.05.21.103564
  • T. Bruna, K.J. Hoff, A. Lomsadze, M. Stanke and M. Borodovsky
    BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database
    NAR Genomics and Bioinformatics 3(1):lqaa108, preprint on biorXive: https://doi.org/10.1101/2020.08.10.245134

2020

  • 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 Ecogology, 29(6):1087-1102, doi: 10.1111/mec.15386
  • K. J. Hoff
    MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs
    Genomics Proteomics and Bioinformatics, 17(5):546-549, doi: 10.1016/j.gpb.2019.05.003
  • N. Herndon, J. Shelton, L. Gerischer, P. Ioannidis, M. Ninova, J. Dönitz, R. M. Waterhouse, C. Liang, C. Damm, J. Siemanowski, P. Kitzmann, J. Ulrich, S. Dippel, G. Oberhofer, Y. Hu, J. Schwirz, M. Schacht, S. Lehmann, A. Montino, N. Posnien, D. Gurska, T. Horn, J. Seibert, I. M. Vargas Jentzsch, K. A. Panfilio, J. Li, E. A. Wimmer, D. Stappert, S. Roth, R. Schröder, Y. Park, M. Schoppmeier, H.-R. Chung, M. Klingler, S. Kittelmann, M. Friedrich, R. Chen, B. Altincicek, A. Vilcinskas, E. Zdobnov, S. Griffiths-Jones, M. Ronshaugen, M. Stanke, S. J. Brown, G. Bucher
    Enhanced genome assembly and a new official gene set for Tribolium castaneum
    BMC Genomics, 21(1):1-13, doi: 10.1186/s12864-019-6394-6
  • 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, 10:125, doi: 10.1038/s41598-019-56907-9

2019

2018

  • J. Lilue, A. G. Doran, I. T. Fiddes, M. Abrudan, J. Armstrong, R. Bennett, W. Chow, J. Collins, S. Collins, A. Czechanski, P. Danecek, M. Diekhans, D.-D. Dolle, M. Dunn, R. Durbin, D. Earl, A. Ferguson-Smith, P. Flicek, J. Flint, A. Frankish, B. Fu, M. Gerstein, J. Gilbert, L. Goodstadt, J. Harrow, K. Howe, X. Ibarra-Soria, M. Kolmogorov, C. J. Lelliott, D. W. Logan, J. Loveland, C. E. Mathews, R. Mott, P. Muir, S. Nachtweide, F. C. P. Navarro, D. T. Odom, N. Park, S. Pelan, S. K. Pham, M. Quail, L. Reinholdt, L. Romoth, L. Shirley, C. Sisu, M. Sjoberg-Herrera, M. Stanke, C. Steward, M. Thomas, G. Threadgold, D. Thybert, J. Torrance, K. Wong, J. Wood, B. Yalcin, F. Yang, D. J. Adams, B. Paten, and T. M. Keane
    Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
    Nature Genetics, 50(11):1574-1583, doi: 10.1038/s41588-018-0223-8
  • K.J. Hoff and M. Stanke
    Predicting Genes in Single Genomes with AUGUSTUS
    Current Protocols in Bioinformatics, doi:10.1002/cpbi.57, manuscript is available for download from Mario's personal homepage.
    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.
  • 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