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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
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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), pages 637-644, doi: 10.1093/bioinformatics/btn013
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Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006)
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
BMC Genome Biology, 7(Suppl 1):S11.
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M. Stanke , O. Schöffmann , B. Morgenstern, S. Waack (2006)
Gene prediction in eukaryotes with a generalized hidden Markov model
that uses hints from external sources
BMC Bioinformatics 7, 62.
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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
- 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
- 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
- Mario Stanke (2003)
Gene
Prediction with a Hidden-Markov Model.
Ph.D. thesis, Universität Göttingen
Genome papers, where AUGUSTUS was used in collaboration:
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
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Tribolium Genome Sequencing Consortium, The genome of the model beetle and pest Tribolium castaneum. Nature, March 2008.
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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, 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 Vector
Science, doi: 10.1126/science.1138878
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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 Amedeo, 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 (21 September 2007)
Draft Genome of the Filarial Nematode Parasite Brugia malayi
Science, 317 (5845), 1756, doi: 10.1126/science.1145406
User contributed species parameters:
- The cacao parameters for Theobroma cacao were contributed by Don Gilbert.
-
The training annotation files of the following species are a courtesy of Jason Stajich:
Aspergillus fumigatus, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Botrytis cinerea, Candida albicans,
Candida guilliermondii, Candida tropicalis, Chaetomium globosum, Coccidioides immitis, Coprinus cinereus, Cryptococcus neoformans gattii,
Cryptococcus neoformans neoformans, Debaryomyces hansenii, Encephalitozoon cuniculi, Eremothecium gossypii, Fusarium graminearum,
Histoplasma capsulatum, Kluyveromyces lactis, Laccaria bicolor, Lodderomyces elongisporus, Magnaporthe grisea, Neurospora crassa,
Phanerochaete chrysosporium, Pichia stipitis, Rhizopus oryzae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Ustilago maydis, Yarrowia lipolytica.
-
The training for lamprey (Petromyzon marinus) was performed by Falk Hildebrand and Shigehiro Kuraku, based on the
genome assembly (PMAR3.0) provided by the Genome Sequencing Center at Washington University School of Medicine (WUGSC)
in St. Louis. The training is described in:
Molecular Evolution in the Lamprey Genomes and Its Relevance to the Timing of Whole Genome Duplications
T. Manousaki, H. Qiu, M. Noro, F. Hildebrand, A. Meyer and S. Kuraku in 'Jawless Fishes of the World, Volume 1', Cambridge Scholars Publishing
-
The training for elephant shark (Callorhinchus milii) was performed by Tereza Manousaki and Shigehiro Kuraku, based on the genome assembly
(made up of 1.4x whole genome shotgun reads) available at http://esharkgenome.imcb.a-star.edu.sg/resources.html and is described in Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes), Briefings in Bioinformatics, 2011.
-
The training for Pneumocystis jirovecii was performed by Marco Pagni, Philippe Hauser et al as described in Hauser PM, Burdet FX, Cisse OH,
Keller L, Taffe P, Sanglard D, Pagni M., Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite
Scavenging Amino Acids from Its Host's Lungs. PLoS One. 2010, Dec 20;5(12):e15152. PubMed PMID: 21188143; PubMed Central PMCID: PMC3004796.
- The parameter training for cacao was done by Don Gilbert (Indiana).
- Parameters for Ancylostoma ceylanicum were trained by Erich Schwarz (Cornell University).
- Parameters for Camponotus floridanus (ant) were contributed by Shishir K Gupta.
- Parameters for Apis dorsata were contributed by Francisco Camara Ferreira.