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480 Publications

2018 | Journal Article | PUB-ID: 2918481
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework
Luhmann N, Chauve C, Stoye J, Wittler R (Accepted)
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2919006
Computing the family-free DCJ similarity
Rubert DP, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2018)
BMC Bioinformatics 19(Suppl. 6): 152.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2919005
GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data
Schulz T, Stoye J, Dörr D (2018)
BMC Genomics 19(Suppl. 5): 308.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2919012
Flexible metagenome analysis using the MGX framework
Jaenicke S, Albaum S, Blumenkamp P, Linke B, Stoye J, Goesmann A (2018)
Microbiome 6: 76.
PUB | DOI
 
2018 | Book (Editor) | PUB-ID: 2913920
Comparative Genomics: Methods and Protocols
Setubal JC, Stadler P, Stoye J (Eds) (2018) Methods in Molecular Biology; 1704.
New York: Springer Verlag.
PUB
 
2018 | Book Chapter | PUB-ID: 2913922
Family-Free Genome Comparison
Dörr D, Feijão P, Stoye J (2018)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 331-342.
PUB
 
2018 | Book Chapter | PUB-ID: 2913921
Pan-genome Storage and Analysis Techniques
Zekic T, Holley G, Stoye J (2018)
In: Comparative Genomics. Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 29-53.
PUB
 
2017 | Journal Article | PUB-ID: 2912492 PUB | DOI
 
2017 | Journal Article | PUB-ID: 2909057
Approximating the DCJ distance of balanced genomes in linear time
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Algorithms for Molecular Biology 12: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2017 | Conference Paper | PUB-ID: 2909409
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
PUB | DOI
 
2017 | Conference Paper | PUB-ID: 2907587
Dynamic Alignment-Free and Reference-Free Read Compression
Holley G, Wittler R, Stoye J, Hach F (2017)
In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
PUB | DOI
 
2017 | Book Chapter | PUB-ID: 2913924
Comparative Methods for Reconstructing Ancient Genome Organization
Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (In Press)
In: Comparative Genomics. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology. Springer Verlag.
PUB
 
2017 | Journal Article | PUB-ID: 2909967
New Genome Similarity Measures based on Conserved Gene Adjacencies
Dörr D, Kowada LAB, Soares de Araujo FE, Deshpande S, Dantas S, Moret BME, Stoye J (2017)
Journal of Computational Biology 24(6): 616-634.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2908574
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies
Luhmann N, Lafond M, Thévenin A, Ouangraoua A, Wittler R, Chauve C (2017)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.
PUB | DOI | PubMed | Europe PMC
 
2016 | Conference Paper | PUB-ID: 2903708
A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FV (2016)
In: Proceedings of WABI 2016. LNBI, 9838. 293-306.
PUB | DOI
 
2016 | Conference Paper | PUB-ID: 2900111
New Genome Similarity Measures based on Conserved Gene Adjacencies
Kowada LAB, Doerr D, Dantas S, Stoye J (2016)
In: Research in Computational Molecular Biology. RECOMB 2016. Singh M (Ed); Lecture Notes in Bioinformatics (LNBI), 9649. Springer: 204-224.
PUB | DOI
 
2016 | Journal Article | PUB-ID: 2905930
Finding approximate gene clusters with GECKO 3
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
Nucleic Acids Research 44(20): 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Journal Article | PUB-ID: 2901413
Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging
Gorzolka K, Kölling J, Nattkemper TW, Niehaus K (2016)
PLOS ONE 11(3): 0150208.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2016 | Journal Article | PUB-ID: 2900129
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
Holley G, Wittler R, Stoye J (2016)
Algorithms for Molecular Biology 11: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2016 | Conference Paper | PUB-ID: 2901740
The SCJ small parsimony problem for weighted gene adjacencies
Luhmann N, Thévenin A, Ouangraoua A, Wittler R, Chauve C (2016)
In: Proceedings 12th International Symposium, ISBRA 2016. Lecture Notes in Computer Science, 9683. Springer International Publishing: 200-210.
PUB | DOI | arXiv
 

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