gobics.de [ Mario Stanke ]

Dr. Mario Stanke Institut für Mikrobiologie und Genetik Abteilung für Bioinformatik Goldschmidtstr. 1 37077 Göttingen Germany phone: +49 551 39 14926 fax: +49 551 39-14929 Email: mstanke@gwdg.de This is my old homepage. Since July 2010 I am working as professor for Bioinformatics at the University of Greifswald.

• Gene Finding in Eukaryotes
• Transcript Quantification
• Recombination in HIV
• Coalescence Theory for Recombining Sequences
• Algorithms for Next Generation Sequencing and RNA-Seq
• Predicting Protein-Protein-Interfaces
• Proteogenomics
• Pharmacogenetics

• Research grant STA 1009/5-1 of the Deutsche Forschungsgemeinschaft "Classification of HIV-1 Using Coalescent Theory"
• Research grant WA766/6-1 of the Deutsche Forschungsgemeinschaft "Verbesserung der Vorhersage neuer Mitglieder von Proteinfamilien in eukaryotischen Genomen am Beispiel der Analyse der Kinesin-Motorproteine", together with Stephan Waack and Martin Kollmar

• AUGUSTUS: Gene prediction in eukaryotes
  
• jpHMM: Detecting recombination in HIV
• ARGUS: Coalescent model with recombination for HIV

• A list of topics for possible student projects (theses or lab roation) can be found on my stud.ip page.
• Lecture about Gene Prediction, Algorithms for Bioinformatics II, SS 2010
• Probabilistische Modellierung in der Angewandten Informatik (SS 2008) Folien zu jpHMM, CRFs
• Molecular Biology Methods Course: The UCSC Genome Browser (WS 2007/2008)
• Statistik für Biologen (SS 2005)
• Algorithmen der Bioinformatik II (WS 2005/2006)
• Molecular Biology Methods Course: Gene Prediction (WS 2005/2006)
• Einführung in die Bioinformatik: Genvorhersage (WS 2005/2006)

• 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 published ahead of print June 14, doi:10.1073/pnas.1003391107
• 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
• 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, Zeitungsartikel
• 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
• 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, accepted
• 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
• 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
• 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 analysis
  Future Generation Computer Systems, Vol.25, No 3, 337 - 345
• 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
• 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 project
  BMC Bioinformatics, 9:549, doi:10.1186/1471-2105-9-549
• 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
• 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 species
  BMC Bioinformatics, 9:278, doi: 10.1186/1471-2105-9-278
• The Tribolium Genome Sequencing Consortium (2008)
  The genome of the beetle developmental model and pest Tribolium castaneum
  Nature 452, 949-955.
• 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
• 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.
• 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
  Planta, doi: 10.1007/s00425-007-0622-z
• 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 malayi
  Science, 317 (5845), 1756, doi: 10.1126/science.1145406
• 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 Vector
  Science, doi: 10.1126/science.1138878
• 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 2007
  Nucleic Acids Research, doi: 10.1093/nar/gkl928
• 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.
• 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
• 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.
• 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.
• 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.
• 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, (2004)
  "Sequential selection of random vectors under a sum constraint",
  Journal of Applied Probability, 41(1), 131-146: preprint
• 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 : preprint

• 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.

• Xin Xing, Mario Stanke
  A Fully Automatic AUGUSTUS Pipeline for Eukaryotic Genome Annotation Based on ESTs
  ISMB/ECCB 2009, Stockholm, Sweden
• A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, M. Stanke
  jpHMM: Improving the reliability of recombination prediction in HIV-1,
  16th International HIV Dynamics & Evolution 2009, Oxford, UK
• A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke
  jpHMM: A jumping profile HMM to detect recombinations in HIV-1,
  European Conference on Computational Biology, ECCB 2008, Cagliari, Italy
• A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke
  jpHMM: A jumping profile HMM to predict recombinations in HIV-1,
  German Conference on Bioinformatics, GCB 2008, Dresden, Germany
• A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke
  jpHMM: Detecting recombinations in HIV-1,
  15th International HIV Dynamics & Evolution 2008, Santa Fe, USA
• A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke
  A Jumping Profile HMM to predict recombinations in HIV-1 sequences,
  13th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology 2007, Lisbon, Portugal
• Kreuter P., Stanke M., Borchardt A., Meier J., Neuhäuser-Berthold M. and Pudel V. (2005)
  "Einfluss von Gewichtsverlust und Fettreduktion auf die Fettpräferenz Adipöser." (Abstract).
  Proceedings of the German Nutrition Society, 7, 30-31
• Anne-Kathrin Schultz and Mario Stanke (2004)
  "A Jumping Profile HMM for Remote Protein Homology Detection",
  Proceedings of the German Conference on Bioinformatics, 91-92
• Kreuter P., Stanke M., Borchardt A., Neuhäuser-Berthold M. and Pudel V. (2004)
  "Einfluss von PROP-Taster-Status auf den Abnahmeerfolg Adipöser" (Abstract)
  Aktuelle Ernährungsmedizin, 29:291
• Kreuter P., Stanke M., Borchardt A., Neuhäuser-Berthold M. and Pudel V. (2004)
  "PROP-Taster-Status bei Adipösen im Vergleich zu Normalgewichtigen" (Abstract).
  Aktuelle Ernährungsmedizin, 29:291-292
• Kreuter P., Stanke M., Ellrott T, Meier J., Neuhäuser-Berthold M. and Pudel V. (2004)
  "Einfluss von PROP-Taster-Status auf die Fettwahrnehmung und Fettpräferenz
  sowie auf die Fettzufuhr bei Normalgewichtigen" (Abstract).
  Proceedings of the German Nutrition Society, 6, 79-80
• Kreuter P., Ellrott T., Stanke M., Neuhäuser-Berthold M. and Pudel V. (2002)
  "Einfluss von PROP-Taster-Status und gezügeltem Essverhalten auf den BMI stark Adipöser
  zu Beginn eines einjährigen ambulanten Gewichtsreduktionsprogramms" (Abstract).
  Aktuelle Ernährungsmedizin, 27, 341-342
  

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

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

Last modified:  August 4th, 2010