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vom 14.7.2021
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Gerlach, Wolfgang ; Jünemann, Sebastian ; Tille, Felix ; Goesmann, Alexander ; Stoye, Jens
In: BMC Bioinformatics, Jg. 10 H. 1, S. 430 ff.
2009
The double cut and join operation and its applications to genome rearrangements
Zakotnik, Julia
2008
Suffix Tree Construction and Storage with Limited Main Memory
Schürmann, Klaus-Bernd ; Stoye, Jens
2003
Suffix arrays in theory and practice
Schürmann, Klaus-Bernd
2007
Simple and flexible detection of contiguous repeats using a suffix tree
Stoye, Jens ; Gusfield, Dan
In: Theoretical Computer Science, Jg. 270 H. 1-2, S. 843-856
2002
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz, Stefan ; Choudhuri, Jomuna V. ; Ohlebusch, Enno ; Schleiermacher, Chris ; Stoye, Jens ; Giegerich, Robert
In: Nucleic Acids Research, Jg. 29 H. 22, S. 4633-4642
2001
QAlign: quality-based multiple alignments with dynamic phylogenetic analysis
Sammeth, Michael ; Rothgänger, Jörg ; Esser, Wolfram ; Albert, Jürgen ; Stoye, Jens ; Harmsen, Dag
In: BIOINFORMATICS, Jg. 19 H. 12, S. 1592-1593
2003
Probabilistic arithmetic automata : applications of a stochastic computational framework in biological sequence analysis
Herms, Inke
2009
Phylogeny-based analysis of gene clusters
Wittler, Roland
2010
Phylogenetic Comparative Assembly
Husemann, Peter ; Stoye, Jens
In: Algorithms for Molecular Biology, Jg. 5 H. 1
2010
Phylogenetic classification of short environmental DNA fragments
Krause, Lutz ; Diaz, Naryttza N. ; Goesmann, Alexander ; Kelley, Scott ; Nattkemper, Tim Wilhelm ; Rohwer, Forest ; Edwards, Robert A. ; Stoye, Jens
In: Nucleic Acids Research, Jg. 36 H. 7, S. 2230-2239
2008
Online Abelian Pattern Matching
Ejaz, Tahir ; Rahmann, Sven ; Stoye, Jens
2008
On the Similarity of Sets of Permutations and its Applications to Genome Comparison
Bergeron, Anne ; Stoye, Jens
2003
On Common Intervals with Errors
Chauve, Cedric ; Diekmann, Yoan ; Heber, Steffen ; Mixtacki, Julia ; Rahmann, Sven ; Stoye, Jens
2006
New algorithms and lower bounds for sequential-access data compression
Gagie, Travis
2009
MeltDB : a software platform for the analysis and integration of metabolomics experiment data
Neuweger, Heiko
2009
Linear time algorithms for finding and representing all the tandem repeats in a string
Gusfield, Dan ; Stoye, Jens
In: Journal of computer and system sciences, Jg. 69 H. 4, S. 525-546
2004
Large scale hierarchical clustering of protein sequences
Krause, Antje ; Stoye, Jens ; Vingron, Martin
In: BMC Bioinformatics, Jg. 6 H. 1
2005
Integrated multiple sequence alignment
Sammeth, Michael
2005

vom 13.7.2021
GISMO - gene identification using a support vector machine for ORF classification
Krause, Lutz ; McHardy, Alice C. ; Nattkemper, Tim Wilhelm ; Pühler, Alfred ; Stoye, Jens ; Meyer, Folker
In: Nucleic Acids Research, Jg. 35 H. 2, S. 540-549
2007
From single genomes to natural microbial communities : novel methods for the high-throughput analysis of genomic sequences
Krause, Lutz
2007
Flexible protein annotation with sequence- and secondary structure information
Bannert, Constantin
2008
Efficient implementation of lazy suffix trees
Giegerich, Robert ; Kurtz, Stefan ; Stoye, Jens
In: SOFTWARE-PRACTICE & EXPERIENCE, Jg. 33 H. 11, S. 1035-1049
2003
Efficient algorithms for gene cluster detection in prokaryotic genomes
Schmidt, Thomas
2005
Divide-and-conquer multiple alignment with segment-based constraints
Sammeth, Michael ; Morgenstern, Burkhard ; Stoye, Jens
In: BIOINFORMATICS, Jg. 19 H. Suppl 2, S. ii189-ii195
2003
Counting Suffix Arrays and Strings
Schürmann, Klaus-Bernd ; Stoye, Jens
2005
Correction: 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. 1
2004
Computational methods for splice site prediction
Taher, Leila
2006
Comparing organisms on the level of metabolism
Oehm, Sebastian
2009
Comparative 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, Alexander
In: NUCLEIC ACIDS RESEARCH, Jg. 36 H. Web Server, S. W433-W437
2008
Common intervals and sorting by reversals: a marriage of necessity
Bergeron, Anne ; Heber, Steffen ; Stoye, Jens
In: Bioinformatics, Jg. 18 H. Suppl 2, S. S54-S63
2002
Clustering biological data by unraveling hidden transitive substructures
Wittkop, Tobias
2010
Biological applications for de Bruijn subgraphs and interval group testing
Quitzau, José Augusto Amgarten
2010
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. 1
2004
BACCardI - 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. 853-859
2005
Approximate common intervals based gene cluster models
Jahn, Katharina
2010
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth, Michael ; Stoye, Jens
2005
Algorithmic complexity of protein identification: combinatorics of weighted strings
Cieliebak, Mark ; Erlebach, Thomas ; Lipták, Zsuzsanna ; Stoye, Jens ; Welzl, Emo
In: Discrete Applied Mathematics, Jg. 137 H. 1, S. 27-46
2004
A space efficient representation for sparse de Bruijn subgraphs
Quitzau, José Augusto Amgarten ; Stoye, Jens
2008
A novel approach to remote homology detection: jumping alignments
Spang, Rainer ; Rehmsmeier, Marc ; Stoye, Jens
In: Journal of Computational Biology, Jg. 9 H. 5, S. 747-760
2002