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. 27-46An iterative method for faster sum-of-pairs multiple sequence alignment
Reinert, Knut ; Stoye, Jens ; Will, TorstenIn: Bioinformatics, Jg. 16 H. 9, S. 808-814Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
Rubert, Diego ; Martinez, Fábio Henrique Viduani ; Stoye, Jens ; Dörr, DanielIn: BMC Genomics, Jg. 21 H. Suppl. 2Approximating the DCJ distance of balanced genomes in linear time
Rubert, Diego ; Feijão, Pedro ; Dias Vieira Braga, Marília ; Stoye, Jens ; Martinez, Fábio Henrique ViduaniIn: Algorithms for Molecular Biology, Jg. 12 H. 1BACCardI - 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. 1Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
Holley, Guillaume ; Wittler, Roland ; Stoye, JensIn: Algorithms for Molecular Biology, Jg. 11 H. 1Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Hoffmann, Nils ; Keck, Matthias ; Neuweger, Heiko ; Wilhelm, Mathias ; Högy, Petra ; Niehaus, Karsten ; Stoye, JensIn: BMC Bioinformatics, Jg. 13 H. 1Common 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-W437The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110
Schwientek, Patrick ; Szczepanowski, Rafael ; Rückert, Christian ; Kalinowski, Jörn ; Klein, Andreas ; Selber, Klaus ; Wehmeier, Udo F. ; Stoye, Jens ; Pühler, AlfredIn: BMC Genomics, Jg. 13 H. 1Computing the family-free DCJ similarity
Rubert, Diego ; Hoshino, Edna A. ; Dias Vieira Braga, Marília ; Stoye, Jens ; Martinez, Fábio Henrique ViduaniIn: BMC Bioinformatics, Jg. 19 H. Suppl. 6Contig selection in physical mapping
Heber, Steffen ; Stoye, Jens ; Frohme, Marcus ; Hoheisel, Jörg ; Vingron, MartinIn: Journal of Computational Biology, Jg. 7 H. 3-4, S. 395-408Correction: 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. 1Detecting High Scoring Local Alignments in Pangenome Graphs
Schulz, Tizian ; Wittler, Roland ; Rahmann, Sven ; Hach, Faraz ; Stoye, JensIn: Bioinformatics, Jg. 37 H. 16, S. 2266-2274Divide-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. 1035-1049Finding all maximal perfect haplotype blocks in linear time
Alanko, Jarno ; Bannai, Hideo ; Cazaux, Bastien ; Peterlongo, Pierre ; Stoye, JensIn: Algorithms for Molecular Biology, Jg. 15Gene family assignment-free comparative genomics
Dörr, Daniel ; Thévenin, Annelyse ; Stoye, JensIn: BMC Bioinformatics, Jg. 13 H. Suppl 19: Proc. of RECOMB-CG 2012Genomic distance under gene substitutions
Dias Vieira Braga, Marília ; Machado, Raphael ; Ribeiro, Leonardo C. ; Stoye, JensIn: BMC Bioinformatics, Jg. 12 H. Suppl 9: Proc. of RECOMB-CG 2011