Siehe mein Profil bei Google Scholar für eine Liste, die Zitierungen einschließt.

Artikel in Journalen

  1. Stanke M, Bruhn W, Becker F, Hoff KJ. (2019), VARUS: Sampling Complementary RNA Reads from the Sequence Read Archive. bioRxiv. 2019 April 13, doi: 10.1101/608737
  2. Kristin Franke, Isabell Karl, Tonatiuh Pena Centeno, Barbara Feldmeyer, Christian Lassek, Vicencio Oostra, Katharina Riedel, Mario Stanke, Christopher W. Wheat, Klaus Fischer (2019), Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimationBMC Evolutionary Biology, 19(1):32. doi: 10.1186/s12862-019-1362-y
  3. Jingtao Lilue, Anthony G. Doran, Ian T. Fiddes, Monica Abrudan, Joel Armstrong, Ruth Bennett, William Chow, Joanna Collins, Stephan Collins, Anne Czechanski, Petr Danecek, Mark Diekhans, Dirk-Dominik Dolle, Matt Dunn, Richard Durbin, Dent Earl, Anne Ferguson-Smith, Paul Flicek, Jonathan Flint, Adam Frankish, Beiyuan Fu, Mark Gerstein, James Gilbert, Leo Goodstadt, Jennifer Harrow, Kerstin Howe, Ximena Ibarra-Soria, Mikhail Kolmogorov, Chris J. Lelliott, Darren W. Logan, Jane Loveland, Clayton E. Mathews, Richard Mott, Paul Muir, Stefanie Nachtweide, Fabio C. P. Navarro, Duncan T. Odom, Naomi Park, Sarah Pelan, Son K. Pham, Mike Quail, Laura Reinholdt, Lars Romoth, Lesley Shirley, Cristina Sisu, Marcela Sjoberg-Herrera, Mario Stanke, Charles Steward, Mark Thomas, Glen Threadgold, David Thybert, James Torrance, Kim Wong, Jonathan Wood, Binnaz Yalcin, Fengtang Yang, David J. Adams, Benedict Paten, and Thomas M. Keane (2018), 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.
  4. Neetika Nath, Jennifer Esche, Jessica Müller, Lars Jensen, Matthias Port, Mario Stanke, Lars Kaderali, Harry Scherthan, and Andreas Kuss (2018), Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva FibroblastsHealth Physics, 115:1, pages 151-160
  5. Ian T. Fiddes, Joel Armstrong, Mark Diekhans, Stefanie Nachtweide, Zev N. Kronenberg, Jason G. Underwood, David Gordon, Dent Earl, Thomas Keane, Evan E. Eichler, David Haussler, Mario Stanke, and Benedict Paten (2018), Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation. Genome Research, June 8, doi:10.1101/gr.233460.117
  6. David Thybert, Maša Roller, Fábio C.P. Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C. Karn, Christina M. Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Stefanie Nachtweide, Michael A. Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David J. Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas M. Keane, Duncan T. Odom, and Paul Flicek (2018), 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
  7. Evelyn E Schwager, Prashant P Sharma, Thomas Clarke, Daniel J Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D Buffry, Hsu Chao, Huyen Dinh, HarshaVardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G Extavour, Peter Funch, Jessica Garb, Luis Gonzalez, Vanessa L Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel ST Hughes, Ralf Janssen, Sandra L Lee, Ignacio Maeso, Shwetha C Murali, Donna M Muzny, Rodrigo Nunes da Fonseca, Christian LB Paese, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schoenauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, John H Werren, Carsten Wolff, Kim C Worley, Gregor Bucher, Richard A Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A Ayoub, Nikola-Michael Prpic, Jean-Francois Flot, Nico Posnien, Stephen Richards, Alistair P McGregor (2017), The house spider genome reveals an ancient whole-genome duplication during arachnid evolutionBMC Biology, 15:62, DOI 10.1186/s12915-017-0399-x
  8. Shuquing Xu, Thomas Brockmöller, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke, Haibao Tang, Eric Lyons, Priyanka Pandey, Shree P. Pandey, Bernd Timmermann, Emmanuel Gaquerel, Ian T. Baldwin (2017). Wild tobacco genomes reveal the evolution of nicotine biosynthesis. PNAS, doi:10.1073/pnas.1700073114
  9. Cai, B., Li, B., Kiga, N., Thusberg, J., Bergquist, T., Chen, Y.-C., Niknafs, N., Carter, H., Tokheim, C., Beleva-Guthrie, V., Douville, C., Bhattacharya, R., Grace Yeo, H. T., Fan, J., Sengupta, S., Kim, D., Cline, M., Turner, T., Diekhans, M., Zaucha, J., Pal, L. R., Cao, C., Yu, C.-H., Yin, Y., Carraro, M., Giollo, M., Ferrari, C., Leonardi, E., Tosatto, S. C.E., Bobe, J., Ball, M., Hoskins, R., Repo, S., Church, G., Brenner, S. E., Moult, J., Gough, J., Stanke, M., Karchin, R. and Mooney, S. D (2017). Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Human Mutation. doi:10.1002/humu.23265
  10. Kerry L Gendreau, Robert A Haney, Evelyn E Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards, Jessica E Garb (2017). House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity. BMC Genomics, 18:178, doi:10.1186/s12864-017-3551-7
  11. Stefanie König, Lars Romoth, Lizzy Gerischer, Mario Stanke (2016), Simultaneous Gene Finding in Multiple Genomes. Bioinformatics, 32 (22): 3388-3395, doi: 10.1093/bioinformatics/btw494
  12. Katharina Hoff, Simone Lange, Alex Lomsadze, Mark Borodovsky, Mario Stanke (2015), BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics, 32 (5): 767-769, doi:10.1093/bioinformatics/btv661
  13. Julia Ulrich, Van Dao, Upalparna Majumdar, Christian Schmitt-Engel, Jonas Schwirz, Dorothea Schultheis, Nadi Ströhlein, Nicole Troelenberg, Daniela Grossmann, Tobias Richter, Jürgen Dönitz, Lizzy Gerischer, Gérard Leboulle, Andreas Vilcinskas, Mario Stanke, Gregor Bucher (2015), Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target. BMC Genomics, 16:674
  14. Katharina Hoff, Mario Stanke (2015), Current Methods for Automated Annotation of Protein-Coding Genes. Current Opinion in Insect Science, doi:10.1016/j.cois.2015.02.008, p. 8-14
  15. Torsten Wierschin, Keyu Wang, Marlon Welter, Stephan Waack, Mario Stanke (2015), Combining Features in a Graphical Model to Predict Protein Binding Sites. PROTEINS: Structure, Function, and Bioinformatics, 83(5):844-852, doi:10.1002/prot.24775
  16. Dippel S, Oberhofer G, Kahnt J, Gerischer L, Opitz L, Schachtner J, Stanke M, Schütz S, Wimmer EA, Angeli S. (2014), 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
  17. Ian K Blaby, Crysten E Blaby-Haas, Nicolas Tourasse, Erik FY Hom, David Lopez, Munevver Aksoy, Arthur Grossman, James Umen, Susan Dutcher, Mary Porter, Stephen King, George B Witman, Mario Stanke, Elizabeth H Harris, David Goodstein, Jane Grimwood, Jeremy Schmutz, Olivier Vallon, Sabeeha S Merchant, Simon Prochnik (2014), The Chlamydomonas genome project: a decade on. Trends in Plant Science, 19(10)
  18. Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke, Stephan Waack (2014), CRF-based models of protein surfaces improve protein-protein interaction site predictionsBMC Bioinformatics, 15:277
  19. Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RF, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Van Vaerenbergh M, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, Gibbs RA (2014), Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics, 15:86
  20. Tran VT, Braus-Stromeyer SA, Kusch H, Reusche M, Kaever A, Kühn A, Valerius O, Landesfeind M, Aßhauer K, Tech M, Hoff K, Pena-Centeno T, Stanke M,Lipka V, Braus GH (2014), Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.The New phytologist, doi: 10.1111/nph.12671
  21. Sandra Van der Auwera, Ingo Bulla, Mario Ziller, Anne Pohlmann, Timm Harder, Mario Stanke (2014), ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs. PLoS One, 9(1):e84558
  22. Steijger T, Abril JF, Engström PG, Kokocinski F; Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Engström PG, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Kokocinski F, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, Niermann P, Rätsch G, Reymond A, Ribeca P, Richard H, Rougemont J, Rozowsky J, Sammeth M, Sboner A, Schulz MH, Searle SM, Solorzano ND, Solovyev V, Stanke M, Steijger T, Stevenson BJ, Stockinger H, Valsesia A, Weese D, White S, Wold BJ, Wu J, Wu TD, Zeller G, Zerbino D, Zhang MQ, Hubbard TJ, Guigó R, Harrow J, Bertone P. (2013), Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, Dec;10(12):1177-84. doi: 10.1038/nmeth.2714
  23. Katharina J. Hoff and Mario Stanke (2013), WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Research, 10.1093/nar/gkt418
  24. Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP (2013), Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote. Science, 8 March 2013: Vol. 339 no. 6124 pp. 1207-1210
  25. Florian Martin, Lucien Bovet, Audrey Cordier, Mario Stanke, Irfan Gunduz, Manuel Peitsch and Nikolai 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
  26. Anne-Kathrin Schultz, Ingo Bulla, Mariama Abdou-Chekaraou, Emmanuel Gordien, Burkhard Morgenstern, Fabien Zoulim, Paul Deny and Mario Stanke (2012), jpHMM: Recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Res, web server issue, 40(W1):W193-W198
  27. Raymond F, Boisvert S, Roy G, Ritt JF, Légaré D, Isnard A, Stanke M, Olivier M, Tremblay MJ, Papadopoulou B, Ouellette M, Corbeil J (2011), Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res. 2011 Oct 13
  28. Thomas Unterthiner, Anne-Kathrin Schultz, Jan Bulla, Burkhard Morgenstern, Mario Stanke and Ingo Bulla (2011), Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. BMC Bioinformatics, 12:93
  29. Michael Specht, Mario Stanke, Mia Terashima, Bianca Naumann-Busch, Ingrid Hanßen, Ricarda Höhner, Erik F.Y. Hom, Chun Liang, and Michael 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):1814-23
  30. Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011), A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics, doi: 10.1093/bioinformatics/btr010
  31. Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. (2010), HIV classification using the coalescent theory. Bioinformatics, 26(11):1409-15
  32. Peter Arensburger, Karine Megy, Robert M. Waterhouse, Jenica Abrudan, Paolo Amedeo, Beatriz Antelo, Lyric Bartholomay, Shelby Bidwell, Elisabet Caler, Francisco Camara, Corey L. Campbell, Kathryn S. Campbell, Claudio Casola, Marta T. Castro, Ishwar Chandramouliswaran, Sinéad B. Chapman, Scott Christley, Javier Costas, Eric Eisenstadt, Cedric Feschotte, Claire Fraser-Liggett, Roderic Guigo, Brian Haas, Martin Hammond, Bill S. Hansson, Janet Hemingway, Sharon R. Hill, Clint Howarth, Rickard Ignell, Ryan C. Kennedy, Chinnappa D. Kodira, Neil F. Lobo, Chunhong Mao, George Mayhew, Kristin Michel, Akio Mori, Nannan Liu, Horacio Naveira, Vishvanath Nene, Nam Nguyen, Matthew D. Pearson, Ellen J. Pritham, Daniela Puiu, Yumin Qi, Hilary Ranson, Jose M. C. Ribeiro, Hugh M. Roberston, David W. Severson, Martin Shumway, Mario Stanke, Robert L. Strausberg, Cheng Sun, Granger Sutton, Zhijian (Jake) Tu, Jose Manuel C. Tubio, Maria F. Unger, Dana L. Vanlandingham, Albert J. Vilella, Owen White, Jared R. White, Charles S. Wondji, Jennifer Wortman, Evgeny M. Zdobnov, Bruce Birren, Bruce M. Christensen, Frank H. Collins, Anthony Cornel, George Dimopoulos, Linda I. Hannick, Stephen Higgs, Gregory C. Lanzaro, Daniel Lawson, Norman H. Lee, Marc A. T. Muskavitch, Alexander S. Raikhel, and Peter W. Atkinson (2010), Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics. Science 330 (6000), 86
  33. AP Chan, J Crabtree, Q Zhao, H Lorenzi, J Orvis, D Puiu, A Melake-Berhan, KM Jones, J Redman, G Chen, EB Cahoon, M Gedil, M Stanke, BJ Haas, JR Wortman, CM Fraser-Liggett, J Ravel, PD Rabinowicz. (2010), Draft genome sequence of the oilseed species Ricinus communis. Nature Biotechnology, 28:951–956, doi:10.1038/nbt.1674
  34. Mansi Srivastava, Oleg Simakov, Jarrod Chapman, Bryony Fahey, Marie E. A. Gauthier, Therese Mitros, Gemma S. Richards, Cecilia Conaco, Michael Dacre, Uffe Hellsten, Claire Larroux, Nicholas H. Putnam, Mario Stanke, Maja Adamska, Aaron Darling, Sandie M. Degnan, Todd H. Oakley, David C. Plachetzki, Yufeng Zhai, Marcin Adamski, Andrew Calcino, Scott F. Cummins, David M. Goodstein, Christina Harris, Daniel J. Jackson, Sally P. Leys, Shengqiang Shu, Ben J. Woodcroft, Michel Vervoort, Kenneth S. Kosik, Gerard Manning, Bernard M. Degnan, and Daniel S. Rokhsar. (2010), The amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466(7307):720–726, August 2010. Presseerklärung 1, Presseerklärung 2, Nature News
  35. Jason E. Stajich, Sarah K. Wilke, Dag Ahren, Chun Hang Au, Bruce W. Birren, Mark Borodovsky, Claire Burns, Björn Canbäck, Lorna A. Casselton, C.K. Cheng, Jixin Deng, Fred S. Dietrich, David C. Fargo, Mark L. Farman, Allen C. Gathman, Jonathan Goldberg, Roderic Guigo, Patrick J. Hoegger, James B. Hooker, Ashleigh Huggins, Timothy Y. James, Takashi Kamada, Sreedhar Kilaru, Chinnapa Kodira, Ursula Kües, Doris Kupfer, H.S. Kwan, Alexandre Lomsadze, Weixi Li, Walt W. Lilly, Li-Jun Ma, Aaron J. Mackey, Gerard Manning, Francis Martin, Hajime Muraguchi, Donald O. Natvig, Heather Palmerini, Marilee A. Ramesh, Cathy J. Rehmeyer, Bruce A. Roe, Narmada Shenoy, Mario Stanke, Vardges Ter-Hovhannisyan, Anders Tunlid, Rajesh Velagapudi, Todd J. Vision, Qiandong Zeng, Miriam E. Zolan and Patricia J. Pukkila (2010), Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus), PNAS, doi:10.1073/pnas.1003391107
  36. Ming Zhang, Brian Foley, Anne-Kathrin Schultz, Jennifer Macke, Ingo Bulla, Mario Stanke, Burkhard Morgenstern, Bette Korber and Thomas Leitner (2010), The role of recombination in the emergence of a complex and dynamic HIV epidemic, Retrovirology 7:25, doi:10.1186/1742-4690-7-25
  37. The International Aphid Genomics Consortium (2010), Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biology 8(2): e1000313. doi:10.1371/journal.pbio.1000313
  38. The Nasonia Genome Working Group (2010), Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species, Science, 15 January 2010, pp. 343-348, Science magazine audio podcast, Zeitungsartikel
  39. Susanta K. Behura, Mario Stanke, Christopher A. Desjardins, John H. Werren, David W. Severson (2009), Comparative Analysis of Nuclear tRNA Genes of Nasonia vitripennis with Apis mellifera and Other Sequenced Arthropods, Insect Molecular Biology, 19 (s1), 49 - 58
  40. Matthew Berriman, Brian J. Haas, Philip T. LoVerde, R. Alan Wilson, Gary P. Dillon, Gustavo C. Cerqueira, Susan T. Mashiyama, Bissan Al-Lazikani, Luiza F. Andrade, Peter D. Ashton, Martin A. Aslett, Daniella C. Bartholomeu, Gaelle Blandin, Conor R. Caffrey, Avril Coghlan, Richard Coulson, Tim A. Day, Art Delcher, Ricardo DeMarco, Appolinaire Djikeng, Tina Eyre, John A. Gamble, Elodie Ghedin, Yong Gu, Christiane Hertz-Fowler, Hirohisha Hirai, Yuriko Hirai, Robin Houston, Alasdair Ivens, David A. Johnston, Daniela Lacerda, Camila D. Macedo, Paul McVeigh, Zemin Ning, Guilherme Oliveira, John P. Overington, Julian Parkhill, Mihaela Pertea, Raymond J. Pierce, Anna V. Protasio, Michael A. Quail, Marie-Adele Rajandream, Jane Rogers, Mohammed Sajid, Steven L. Salzberg, Mario Stanke, Adrian R. Tivey, Owen White, David L. Williams, Jennifer Wortman, Wenjie Wu, Mostafa Zamanian, Adhemar Zerlotini, Claire M. Fraser-Liggett, Barclay G. Barrell, Najib M. El-Sayed (2009), The genome of the blood fluke Schistosoma mansoni, Nature 460, 352-358 (16 July 2009), Presseerklärung
  41. Anne-Kathrin Schultz, Ming Zhang, Ingo Bulla, Thomas Leitner, Bette Korber, Burkhard Morgenstern, Mario Stanke (2009), jpHMM: Improving the reliability of recombination prediction in HIV-1, Nucleic Acids Research, doi: 10.1093/nar/gkp371
  42. Dietmar Sommerfeld, Thomas Lingner, Mario Stanke, Burkhard Morgenstern, Harald Richter (2009), AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysisFuture Generation Computer Systems, Vol.25, No 3, 337 - 345
  43. Natalie E. Castellana, Samuel H. Payne, Zhouxin Shen, Mario Stanke, Vineet Bafna, Steven P. Briggs (2008), Discovery and revision of Arabidopsis genes by proteogenomics, PNAS, 105:21034-21038
  44. Avril Coghlan, Tristan J. Fiedler, Sheldon J. McKay, Paul Flicek, Todd W. Harris, Darin Blasiar, the nGASP Consortium, Lincoln D. Stein (2008), nGASP the nematode genome annotation assessment projectBMC Bioinformatics, 9:549, doi:10.1186/1471-2105-9-549
  45. B. Bunselmeyer, H. J. Laubach, M. Schiller, M. Stanke, T. A. Luger, R. Brehler (2008), Incremental build-up food challenge - a new diagnostic approach to evaluate pseudoallergic reactions in chronic urticaria: a pilot study, Clinical & Experimental Allergy, 39: 116-126, doi: 10.1111/j.1365-2222.2008.03110.x
  46. Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar and Stephan Waack (2008), Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related speciesBMC Bioinformatics, 9:278, doi: 10.1186/1471-2105-9-278
  47. The Tribolium Genome Sequencing Consortium (2008), The genome of the beetle developmental model and pest Tribolium castaneum, Nature 452, 949-955.
  48. Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, 24(5):637, doi: 10.1093/bioinformatics/btn013
  49. D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney, B. Rhead, K. R. Rosenbloom, K. E. Smith, M. Stanke, A. Thakkapallayil, H. Trumbower, T. Wang, A. S. Zweig, D. Haussler, W. J. Kent (2008), The UCSC Genome Browser Database: 2008 update, Nucleic Acids Research, doi: 10.1093/nar/gkm966.
  50. Oesterhelt C, Vogelbein S, Shrestha RP, Stanke M, Weber APM (2007), The genome of the thermoacidophilic red microalga Galdieria sulphuraria encodes a small family of secreted class III peroxidases that might be involved in cell wall modification. Planta, doi: 10.1007/s00425-007-0622-z
  51. Elodie Ghedin, Shiliang Wang, David Spiro, Elisabet Caler, Qi Zhao, Jonathan Crabtree, Jonathan E. Allen, Arthur L. Delcher, David B. Guiliano, Diego Miranda-Saavedra, Samuel V. Angiuoli, Todd Creasy, Paolo Ameedeo, Brian Haas, Najib M. El-Sayed, Jennifer R. Wortman, Tamara Feldblyum, Luke Tallon, Michael Schatz, Martin Shumway, Hean Koo, Steven L. Salzberg, Seth Schobel, Mihaela Pertea, Mihai Pop, Owen White, Geoffrey J. Barton, Clotilde K. S. Carlow, Michael J. Crawford, Jennifer Daub, Matthew W. Dimmic, Chris F. Estes, Jeremy M. Foster, Mehul Ganatra, William F. Gregory, Nicholas M. Johnson, Jinming Jin, Richard Komuniecki, Ian Korf, Sanjay Kumar, Sandra Laney, Ben-Wen Li, Wen Li, Tim H. Lindblom, Sara Lustigman, Dong Ma, Claude V. Maina, David M. A. Martin, James P. McCarter, Larry McReynolds, Makedonka Mitreva, Thomas B. Nutman, John Parkinson, Jose M. Peregri-Alvarez, Catherine Poole, Qinghu Ren, Lori Saunders, Ann E. Sluder, Katherine Smith, Mario Stanke, Thomas R. Unnasch, Jenna Ware, Aguan D. Wei, Gary Weil, Deryck J. Williams, Yinhua Zhang, Steven A. Williams, Claire Fraser-Liggett, Barton Slatko, Mark L. Blaxter, and Alan L. Scott (2007), Draft Genome of the Filarial Nematode Parasite Brugia malayiScience, 317 (5845), 1756, doi: 10.1126/science.1145406
  52. Nene, Vishvanath, Wortman, Jennifer R., Lawson, Daniel, Haas, Brian, Kodira, Chinnappa, Tu, Zhijian Jake, Loftus, Brendan, Xi, Zhijong, Megy, Karyn, Grabherr, Manfred, Ren, Quinghu, Zdobnov, Evgeny M., Lobo, Neil F., Campbell, Kathryn S., Brown, Susan E., Bonaldo, Maria F., Zhu, Jingsong, Sinkins, Steven P., Hogenkamp, David G., Amedo, Paulo, Arsenburger, Peter, Atkinson, Peter W., Bidwell, Shelby, Biedler, Jim, Birney, Ewan, Bruggner, Robert V., Costas, Javier, Coy, Monique R., Crabtree, Jonathan, Crawford, Matt, deBruyn, Becky, DeCaprio, David, Eiglmeier, Karin, Eisenstadt, Eric, El-Dorry, Hamza, Gelbart, William M., Gomes, Suely L., Hammond, Martin, Hannick, Linda I., Hogan, James R., Holmes, Michael H., Jaffe, David, Johnston, Spencer J., Kennedy, Ryan C., Koo, Hean, Kravitz, Saul, Kriventseva, Evgenia V., Kulp, David, LaButti, Kurt, Lee, Edward, Li, Song, Lovin, Diane D., Mao, Chunhong, Mauceli, Evan, Menck, Carlos F. M., Miller, Jason R., Montgomery, Philip, Mori, Akio, Nascimento, Ana L., Naveira, Horacio F., Nusbaum, Chad, O'Leary, Sinead B., Orvis, Joshua, Pertea, Mihaela, Quesneville, Hadi, Reidenbach, Kyanne R., Rogers, Yu-Hui, Roth, Charles W., Schneider, Jennifer R., Schatz, Michael, Shumway, Martin, Stanke, Mario, Stinson, Eric O., Tubio, Jose M. C., VanZee, Janice P., Verjovski-Almeida, Sergio, Werner, Doreen, White, Owen, Wyder, Stefan, Zeng, Qi, Zhao, Qi, Zhao, Yongmei, Hill, Catherine A., Raikhel, Alexander S., Soares, Marcelo B., Knudson, Dennis L., Lee, Norman H., Galagan, James, Salzberg, Steven L., Paulsen, Ian T., Dimopoulos, George, Collins, Frank H., Bruce, Birren, Fraser-Liggett, Claire M., Severson, David W. (2007), Genome Sequence of Aedes aegypti, a Major Arbovirus VectorScience, doi: 10.1126/science.1138878
  53. Kuhn, R. M. , Karolchik, D. , Zweig, A. S. , Trumbower, H. , Thomas, D. J. , Thakkapallayil, A. , Sugnet, C. W. , Stanke, M. , Smith, K. E. , Siep el, A. , Rosenbloom, K. R. , Rhead, B. , Raney, B. J. , Pohl, A. , Pedersen, J. S. , Hsu, F. , Hinrichs, A. S. , Harte, R. A. , Diekhans, M. , Clawson, H. , Bejerano, G. , Barber, G. P. , Baertsch, R. , Haussler, D. , Kent, W. J. (2006), The UCSC genome browser database: update 2007Nucleic Acids Research, doi: 10.1093/nar/gkl928
  54. Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006), "AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome", Genome Biology, 7(Suppl 1):S11.
  55. Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette Korber, Burkhard Morgenstern, Mario Stanke (2006), "A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes". BMC Bioinformatics, 7:265
  56. Mario Stanke , Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern (2006), "AUGUSTUS: ab initio prediction of alternative transcripts", Nucleic Acids Research, 34: W435-W439.
  57. Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette Korber, Burkhard Morgenstern, Mario Stanke (2006), "jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1", Nucleic Acids Research, 34: W463-W465.
  58. Mario Stanke , Oliver Schöffmann , Burkhard Morgenstern, Stephan Waack (2006), "Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources", BMC Bioinformatics 7:62.
  59. Mario Stanke and Burkhard Morgenstern (2005), "AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints", Nucleic Acids Research, 33, W465-W467
  60. Mario Stanke, Rasmus Steinkamp, Stephan Waack and Burkhard Morgenstern (2004), "AUGUSTUS: a web server for gene finding in eukaryotes", Nucleic Acids Research, Vol. 32, W309-W312
  61. Mario Stanke, (2004), "Sequential selection of random vectors under a sum constraint", Journal of Applied Probability, 41(1), 131-146: preprint
  62. Mario Stanke and Stephan Waack (2003), "Gene prediction with a hidden Markov model and a new intron submodel", Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225

Buchkapitel

  1. Stefanie Nachtweide and Mario Stanke (2019), Multi-Genome Annotation with AUGUSTUS. Methods Mol Biol., 1962:139-160. doi: 10.1007/978-1-4939-9173-0_8. PubMed PMID: 31020558. manuscript (PDF)
  2. Hoff KJ, Lomsadze A, Borodovsky M, Stanke M. (2019), Whole-Genome Annotation with BRAKER. Methods Mol Biol., 1962:65-95. doi: 10.1007/978-1-4939-9173-0_5. PubMed PMID: 31020555. manuscript (PDF)
  3. Hoff KJ. ,Stanke M. (2018). Predicting genes in single genomes with AUGUSTUSCurrent Protocols in Bioinformatics, e57. doi: 10.1002/cpbi.57manuscript (PDF)
  4. König S., Romoth L., Stanke M. (2018). Comparative Genome Annotation. In: Setubal J., Stoye J., Stadler P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY
  5. Stanke, M (2010). "Computational Gene Prediction In Eukaryotic Genomes" in the book "Red Algae in the Genomic Age" of the series "Cellular Origin, Life in Extreme Habitats, and Astrobiology", Seckbach, Joseph; Chapman, David J. (Eds.), 1st Edition, XXVIII, 498 p., Hardcover, ISBN: 978-90-481-3794-7

Begutachtete Artikel in Konferenzbänden

  1. M. Zhang, A.-K. Schultz, B. Morgenstern, M. Stanke, B. Korber, T. Leitner,  Greater HIV Genome Diversities Inferred From Re-subtyping of HIV Database Sequences, Proc. German Conference on Bioinformatics (Discovery Notes, Poster Abstracts), pp 5 - 7.
  2. Stefanie König, Lars Romoth, Lizzy Gerischer, and Mario Stanke (2015), Simultaneous gene finding in multiple genomes. PeerJ PrePrints, e1594

Dissertation

  1. Mario Stanke, "Gene Prediction with a Hidden Markov Model" (2004), Ph.D. thesis, Universität Göttingen, Germany, pdf

Diplomarbeit

  1. Mario Stanke, "Sequential Selection under Constraints" (1999), Diplom thesis, Universität Göttingen, Germany