Algorithmic complexity of protein identification: combinatorics of weighted strings
Cieliebak, Mark ; Erlebach, Thomas ; Lipták, Zsuzsanna ; Stoye, Jens ; Welzl, EmoIn: Discrete Applied Mathematics, Jg. 137 H. 1, S. 27-46Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth, Michael ; Stoye, JensBACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Bartels, Daniela ; Kespohl, Sebastian ; Albaum, Stefan ; Drüke, Tanja ; Goesmann, Alexander ; Herold, Julia ; Kaiser, Olaf ; Pühler, Alfred ; Pfeiffer, Friedhelm ; Raddatz, Günter ; Stoye, Jens ; Meyer, Folker ; Schuster, Stephan C.In: Bioinformatics, Jg. 21 H. 7, S. 853-859Benchmarking tools for the alignment of functional noncoding DNA
Pollard, Daniel A. ; Bergman, Casey M. ; Stoye, Jens ; Celniker, Susan E. ; Eisen, Michael B.In: BMC Bioinformatics, Jg. 5 H. 1Biological applications for de Bruijn subgraphs and interval group testing
Quitzau, José Augusto Amgarten2010Common intervals and sorting by reversals: a marriage of necessity
Bergeron, Anne ; Heber, Steffen ; Stoye, JensIn: Bioinformatics, Jg. 18 H. Suppl 2, S. S54-S63Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
Oehm, Sebastian ; Gilbert, David ; Tauch, Andreas ; Stoye, Jens ; Goesmann, AlexanderIn: NUCLEIC ACIDS RESEARCH, Jg. 36 H. Web Server, S. W433-W437Correction: Benchmarking tools for the alignment of functional noncoding DNA
Pollard, Daniel A. ; Bergman, Casey M. ; Stoye, Jens ; Celniker, Susan E. ; Eisen, Michael B.In: BMC Bioinformatics, Jg. 5 H. 1Counting Suffix Arrays and Strings
Schürmann, Klaus-Bernd ; Stoye, JensDivide-and-conquer multiple alignment with segment-based constraints
Sammeth, Michael ; Morgenstern, Burkhard ; Stoye, JensIn: BIOINFORMATICS, Jg. 19 H. Suppl 2, S. ii189-ii195Efficient implementation of lazy suffix trees
Giegerich, Robert ; Kurtz, Stefan ; Stoye, JensIn: SOFTWARE-PRACTICE & EXPERIENCE, Jg. 33 H. 11, S. 1035-1049Flexible protein annotation with sequence- and secondary structure information
Bannert, Constantin2008GISMO - gene identification using a support vector machine for ORF classification
Krause, Lutz ; McHardy, Alice C. ; Nattkemper, Tim Wilhelm ; Pühler, Alfred ; Stoye, Jens ; Meyer, FolkerIn: Nucleic Acids Research, Jg. 35 H. 2, S. 540-549