Mario Stanke

Mario Stanke

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Mario Stanke

Mario Stanke

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Whole-Genome Annotation with BRAKER.

Methods Mol Biol 2019 ;1962:65-95

University of Greifswald, Institute of Mathematics and Computer Science, Greifswald, Germany.

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http://dx.doi.org/10.1007/978-1-4939-9173-0_5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6635606PMC
August 2019

Multi-Genome Annotation with AUGUSTUS.

Methods Mol Biol 2019 ;1962:139-160

Institute of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.

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http://dx.doi.org/10.1007/978-1-4939-9173-0_8DOI Listing
August 2019

Predicting Genes in Single Genomes with AUGUSTUS.

Curr Protoc Bioinformatics 2019 03 22;65(1):e57. Epub 2018 Nov 22.

University of Greifswald, Institute of Mathematics and Computer Science, Greifswald, Germany.

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http://dx.doi.org/10.1002/cpbi.57DOI Listing
March 2019

Comparative Genome Annotation.

Methods Mol Biol 2018 ;1704:189-212

Institut für Mathematik und Informatik, Ernst Moritz Arndt Universität Greifswald, Greifswald, Germany.

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http://link.springer.com/10.1007/978-1-4939-7463-4_6
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http://dx.doi.org/10.1007/978-1-4939-7463-4_6DOI Listing
November 2018

Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva Fibroblasts.

Health Phys 2018 07;115(1):151-160

Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.

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http://dx.doi.org/10.1097/HP.0000000000000880DOI Listing
July 2018

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Genome Res 2018 07 8;28(7):1029-1038. Epub 2018 Jun 8.

Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.233460.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028123PMC
July 2018

Simultaneous gene finding in multiple genomes.

Bioinformatics 2016 11 27;32(22):3388-3395. Epub 2016 Jul 27.

Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, 17487, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860283PMC
November 2016

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

Bioinformatics 2016 03 11;32(5):767-9. Epub 2015 Nov 11.

Ernst Moritz Arndt Universität Greifswald, Institute for Mathematics and Computer Science, 17487 Greifswald, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btv661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078167PMC
March 2016

Combining features in a graphical model to predict protein binding sites.

Proteins 2015 May 14;83(5):844-52. Epub 2015 Mar 14.

Institute of Mathematics and Computer Science, University of Greifswald, 17487, Greifswald, Germany.

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http://dx.doi.org/10.1002/prot.24775DOI Listing
May 2015

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 2014 Dec 18;15:1141. Epub 2014 Dec 18.

Department of Developmental Biology, Georg-August-University Goettingen, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, GZMB, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, Goettingen 37077, Germany.

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http://dx.doi.org/10.1186/1471-2164-15-1141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377858PMC
December 2014

ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

PLoS One 2014 3;9(1):e84558. Epub 2014 Jan 3.

Institute for Mathematics and Computer Science, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084558PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880301PMC
September 2014

CRF-based models of protein surfaces improve protein-protein interaction site predictions.

BMC Bioinformatics 2014 Aug 13;15:277. Epub 2014 Aug 13.

Institute of Computer Science, University of Göttingen, Goldschmidtstr, 7, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1186/1471-2105-15-277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150965PMC
August 2014

Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.

New Phytol 2014 Apr 17;202(2):565-81. Epub 2014 Jan 17.

Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany; Department of Microbiology, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam.

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http://dx.doi.org/10.1111/nph.12671DOI Listing
April 2014

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes.

Nucleic Acids Res 2013 Jul 21;41(Web Server issue):W123-8. Epub 2013 May 21.

Institute for Mathematics and Computer Science, Ernst Moritz Arndt University, 17487 Greifswald, Germany.

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http://dx.doi.org/10.1093/nar/gkt418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692069PMC
July 2013

jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.

Nucleic Acids Res 2012 Jul 16;40(Web Server issue):W193-8. Epub 2012 May 16.

Abteilung für Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1093/nar/gks414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394342PMC
July 2012

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.

BMC Bioinformatics 2011 Apr 11;12:93. Epub 2011 Apr 11.

Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr, 1, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1186/1471-2105-12-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086866PMC
April 2011

A novel hybrid gene prediction method employing protein multiple sequence alignments.

Bioinformatics 2011 Mar 6;27(6):757-63. Epub 2011 Jan 6.

Institute of Computer Science, University of Göttingen, Goldschmidtstrasse 7, Greifswald, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr010DOI Listing
March 2011

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Science 2010 Oct;330(6000):86-8

Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA.

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http://dx.doi.org/10.1126/science.1191864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384PMC
October 2010

HIV classification using the coalescent theory.

Bioinformatics 2010 Jun 16;26(11):1409-15. Epub 2010 Apr 16.

Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btq159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913666PMC
June 2010

The role of recombination in the emergence of a complex and dynamic HIV epidemic.

Retrovirology 2010 Mar 23;7:25. Epub 2010 Mar 23.

Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

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http://dx.doi.org/10.1186/1742-4690-7-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855530PMC
March 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

jpHMM: improving the reliability of recombination prediction in HIV-1.

Nucleic Acids Res 2009 Jul 14;37(Web Server issue):W647-51. Epub 2009 May 14.

Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany.

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http://dx.doi.org/10.1093/nar/gkp371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703979PMC
July 2009

Discovery and revision of Arabidopsis genes by proteogenomics.

Proc Natl Acad Sci U S A 2008 Dec 19;105(52):21034-8. Epub 2008 Dec 19.

Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.0811066106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605632PMC
December 2008

Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.

BMC Bioinformatics 2008 Jun 13;9:278. Epub 2008 Jun 13.

Universität Göttingen, Institut für Informatik, Lotzestr. 16-18, 37083 Göttingen, Germany.

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http://dx.doi.org/10.1186/1471-2105-9-278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442105PMC
June 2008

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Bioinformatics 2008 Mar 24;24(5):637-44. Epub 2008 Jan 24.

Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn013DOI Listing
March 2008

Draft genome of the filarial nematode parasite Brugia malayi.

Science 2007 Sep;317(5845):1756-60

Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1145406
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http://dx.doi.org/10.1126/science.1145406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613796PMC
September 2007

Genome sequence of Aedes aegypti, a major arbovirus vector.

Science 2007 Jun 17;316(5832):1718-23. Epub 2007 May 17.

Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1138878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868357PMC
June 2007

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

Genome Biol 2006 7;7 Suppl 1:S11.1-8. Epub 2006 Aug 7.

Institut für Mikrobiologie und Genetik, Universität Göttingen, Goldschmidtstrasse, 37077 Göttingen, Germany.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2006-7-s1-s11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810548PMC
September 2006

AUGUSTUS: ab initio prediction of alternative transcripts.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W435-9

Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538822PMC
July 2006

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W463-5

Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538796PMC
July 2006

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.

BMC Bioinformatics 2006 May 22;7:265. Epub 2006 May 22.

Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr, 1, 37077 Göttingen, Germany.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525204PMC
May 2006

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

BMC Bioinformatics 2006 Feb 9;7:62. Epub 2006 Feb 9.

lnstitut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1409804PMC
February 2006

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W465-7

Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1093/nar/gki458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160219PMC
July 2005

AUGUSTUS: a web server for gene finding in eukaryotes.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W309-12

University of Göttingen, Institut für Mikrobiologie und Genetik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkh379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441517PMC
July 2004

Gene prediction with a hidden Markov model and a new intron submodel.

Bioinformatics 2003 Oct;19 Suppl 2:ii215-25

Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btg1080DOI Listing
October 2003