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168 Publications

2017 | Journal Article | PUB-ID: 2913556
Bioinformatics for NGS-based metagenomics and the application to biogas research
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, et al. (2017)
Journal of Biotechnology 261(SI): 10-23.
PUB | 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 | Conference Paper | PUB-ID: 2913015
Algorithms for Computing the Family-Free Genomic Similarity under DCJ
Rubert DP, Medeiros GL, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 10562. Springer Verlag: 76-100.
PUB | DOI
 
2017 | Conference Paper | PUB-ID: 2913016
Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery
Schulz T, Stoye J, Dörr D (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
PUB | DOI
 
2017 | Book Chapter | PUB-ID: 2913921
Pan-genome Storage and Analysis Techniques
Zekic T, Holley G, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
2017 | Book Chapter | PUB-ID: 2913922
Family-Free Genome Comparison
Dörr D, Feijão P, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
2017 | Book (Editor) | PUB-ID: 2913920
Comparative Genomics: Methods and Protocols
Setubal JC, Stadler P, Stoye J (Eds) (In Press) Methods in Molecular Biology; 1704.
Springer Verlag.
PUB
 
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 | 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: 2912492 PUB | DOI
 
2017 | Preprint | PUB-ID: 2908521
Faster Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
arXiv: 1702.01280.
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
 
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: 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
 
2016 | Journal Article | PUB-ID: 2900421
Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma
Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, et al. (2016)
Carcinogenesis 37(4): 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 

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