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410 Publikationen

2019 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2935998
Setubal JC, Stoye J, Dutilh BE (Eds) (2019)
Computational Methods for Microbiome Analysis. Frontiers Research Topics.
Lausanne: Frontiers Media.
PUB | Download (ext.)
 
2019 | Preprint | PUB-ID: 2935604
Wittler R (2019)
Alignment- and reference-free phylogenomics with colored de-Bruijn graphs.
arXiv:1905.04165.
PUB | PDF
 
2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
Dörr D, Stoye J (2019)
A Perspective on Comparative and Functional Genomics.
In: Bioinformatics and Phylogenetics. Warnow T (Ed); Computational Biology, 29. Cham: Springer : 361-372.
PUB | DOI
 
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933161
Hassan H, Shanak S (2019)
GOTrapper. A tool to navigate through branches of gene ontology hierarchy.
BMC Bioinformatics 20(1): 20.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones M, Ragan MA, Stoye J, Oleaga A, Emery AM, Webster B, Rollinson D, Gasser RB, McManus DP, Krause L (2019)
Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium.
PLOS Pathogens 15(1): e1007513.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
Schulz T, Stoye J, Dörr D (2018)
GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data.
BMC Genomics 19(Suppl. 5): 308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert D, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FHV (2018)
Computing the family-free DCJ similarity.
BMC Bioinformatics 19(Suppl. 6): 152.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
Luhmann N, Chauve C, Stoye J, Wittler R (2018)
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 15(6): 2094-2100.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932754
Bhatia S, Feijão P, Francis AR (2018)
Position and Content Paradigms in Genome Rearrangements. The Wild and Crazy World of Permutations in Genomics.
BULLETIN OF MATHEMATICAL BIOLOGY 80(12): 3227-3246.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919346
Hagenfeld D, Koch R, Jünemann S, Prior K, Harks I, Eickholz P, Hoffmann T, Kim T-S, Kocher T, Meyle J, Kaner D, Schlagenhauf U, Ehmke B, Harmsen D (2018)
Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis.
PLOS ONE 13(4): e0195534.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Bielefelder E-Dissertation | PUB-ID: 2918485
Holley G (2018)
Pan-genome Search and Storage.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2018 | Bielefelder E-Dissertation | PUB-ID: 2919356
Willing E (2018)
On Distance and Sorting of the Double Cut-and-Join and the Inversion-*indel* Model.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
Cunha L, Diekmann Y, Kowada L, Stoye J (2018)
Identifying Maximal Perfect Haplotype Blocks.
In: Proceedings of BSB 2018. LNBI, 11228. Springer Verlag: 26-37.
PUB | DOI
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
Holley G, Wittler R, Stoye J, Hach F (2018)
Dynamic Alignment-Free and Reference-Free Read Compression.
JOURNAL OF COMPUTATIONAL BIOLOGY 25(7): 825-836.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
Zekic T, Holley G, Stoye J (2018)
Pan-genome Storage and Analysis Techniques.
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
 
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
Dörr D, Feijão P, Stoye J (2018)
Family-Free Genome Comparison.
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 | Herausgeber Sammelwerk | Veröffentlicht | PUB-ID: 2913920
Setubal JC, Stadler P, Stoye J (Eds) (2018)
Comparative Genomics: Methods and Protocols. Methods in Molecular Biology; 1704.
New York: Springer Verlag.
PUB
 
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
Jaenicke S, Albaum S, Blumenkamp P, Linke B, Stoye J, Goesmann A (2018)
Flexible metagenome analysis using the MGX framework.
Microbiome 6: 76.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2912492
Luhmann N, Dörr D, Chauve C (2017)
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.
Microbial Genomics 3(9).
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, Stoye J (2017)
Bioinformatics for NGS-based metagenomics and the application to biogas research.
Journal of Biotechnology 261(SI): 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
Rubert D, Medeiros GL, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Algorithms for Computing the Family-Free Genomic Similarity under DCJ.
In: Comparative Genomics. RECOMB-CG 2017. Meidanis J, Nakhleh L (Eds); Lecture Notes in Bioinformatics, 10562. Cham: Springer Verlag: 76-100.
PUB | DOI
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
Rubert D, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Approximating the DCJ distance of balanced genomes in linear time.
Algorithms for Molecular Biology 12: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2017 | Bielefelder E-Dissertation | PUB-ID: 2909213
Luhmann N (2017)
Phylogenetic assembly of paleogenomes integrating ancient DNA data.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916552
da Silva PH, Machado R, Dantas S, Dias Vieira Braga M (2017)
Genomic Distance with High Indel Costs.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 14(3): 728-732.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.
In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
PUB | DOI
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911814
Dörr D, Balaban M, Feijão P, Chauve C (2017)
The gene family-free median of three.
Algorithms for Molecular Biology 12: 14.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
Faster Jumbled Indexing for Binary Run-Length Encoded Strings.
arXiv: 1702.01280.
PUB
 
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
Holley G, Wittler R, Stoye J, Hach F (2017)
Dynamic Alignment-Free and Reference-Free Read Compression.
In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
PUB | DOI
 
2017 | Sammelwerksbeitrag | Im Druck | PUB-ID: 2913924
Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (In Press)
Comparative Methods for Reconstructing Ancient Genome Organization.
In: Comparative Genomics. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, Springer Verlag.
PUB
 
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
Schulz T, Stoye J, Dörr D (2017)
Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery.
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
PUB | DOI
 
2017 | Zeitschriftenaufsatz | E-Veröff. vor dem Druck | PUB-ID: 2908574
Luhmann N, Lafond M, Thévenin A, Ouangraoua A, Wittler R, Chauve C (2017)
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.
PUB | DOI | PubMed | Europe PMC
 
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
Dörr D, Kowada LAB, Soares de Araujo FE, Deshpande S, Dantas S, Moret BME, Stoye J (2017)
New Genome Similarity Measures based on Conserved Gene Adjacencies.
Journal of Computational Biology 24(6): 616-634.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901477
Ahmed Raza SE, Langenkämper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM (2016)
Robust normalization protocols for multiplexed fluorescence bioimage analysis.
BioData Mining 9(1): 11.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
Finding approximate gene clusters with GECKO 3.
Nucleic Acids Research 44(20): 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
Rubert D, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2016)
A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates.
In: Algorithms in Bioinformatics. WABI 2016. Frith M, Storm Pedersen CN (Eds); Lecture Notes in Bioinformatics, 9838. Cham: Springer: 293-306.
PUB | DOI
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
Holley G, Wittler R, Stoye J (2016)
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.
Algorithms for Molecular Biology 11: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2016 | Bielefelder E-Dissertation | PUB-ID: 2902049
Dörr D (2016)
Gene family-free genome comparison.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2016 | Bielefelder E-Dissertation | PUB-ID: 2906743
Bremges A (2016)
Assembling the microbial dark matter.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900943
Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW (2016)
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.
Frontiers in Genetics 7: 5.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, Lampe G, Clouston A, Thomas J, Stoye J, Hussey DJ, Watson DI, Lord RV, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Grimmond SM, Waddell N, Barbour AP (2016)
Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma.
Carcinogenesis 37(4): 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
Kowada LAB, Doerr D, Dantas S, Stoye J (2016)
New Genome Similarity Measures based on Conserved Gene Adjacencies.
In: Research in Computational Molecular Biology. RECOMB 2016. Singh M (Ed); Lecture Notes in Bioinformatics (LNBI), 9649. Springer: 204-224.
PUB | DOI
 
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901740
Luhmann N, Thévenin A, Ouangraoua A, Wittler R, Chauve C (2016)
The SCJ small parsimony problem for weighted gene adjacencies.
In: Proceedings 12th International Symposium, ISBRA 2016. Lecture Notes in Computer Science, 9683. Springer International Publishing: 200-210.
PUB | DOI | Download (ext.) | arXiv
 
2016 | Konferenzband | Veröffentlicht | PUB-ID: 2912258
Hölldobler S (Ed) (2016)
Genfamilienfreier Genomvergleich.
LNI D-16: 91-100.
PUB | Download (ext.)
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2911748
Krahn T, Wibberg D, Maus I, Winkler A, Pühler A, Poirel L, Schlüter A (2015)
Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.
Genome Announcements 3(4): e00850-15.
PUB | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
Dias Vieira Braga M, Stoye J (2015)
Sorting linear genomes with rearrangements and indels.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 12(3): 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
Viduani Martinez FH, Feijão P, Dias Vieira Braga M, Stoye J (2015)
On the family-free DCJ distance and similarity.
Algorithms for Molecular Biology 10: 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2715682
Henning P, Kuich JL, Hoffmann N, Stefan K (2015)
Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography–mass spectrometry data.
Frontiers in Bioengineering and Biotechnology 2(84).
PUB | DOI | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2766708
Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell P, Borkhardt A, Dugas M, Hu J, Fischer U (2015)
Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients.
Leukemia research.
PUB | DOI | WoS | PubMed | Europe PMC
 
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764612
Wittler R, Marschall T, Schönhuth A, Makinen V (2015)
Repeat- and error-aware comparison of deletions.
Bioinformatics 31(18): 2947-2954.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
Holley G, Wittler R, Stoye J (2015)
Bloom Filter Trie - a data structure for pan-genome storage.
In: Proceedings of WABI 2015. LNBI, 9289. 217-230.
PUB
 
2015 | Bielefelder E-Dissertation | PUB-ID: 2786037
Hilker R (2015)
Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains.
Bielefeld: Bielefeld University.
PUB | Dateien verfügbar
 
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
Meidanis J, Stoye J (Eds) (2015)
Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics.
BMC Bioinformatics 16(Supplement 14).
PUB | Download (ext.)
 
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
Meidanis J, Stoye J (Eds) (2015)
Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics.
BMC Genomics 16(Supplement 10).
PUB | Download (ext.)
 
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
Viduani Martinez FH, Feijão P, Dias Vieira Braga M, Stoye J (2014)
On the family-free DCJ distance.
In: Algorithms in Bioinformatics. WABI 2014. Brown D, Morgenstern B (Eds); Lecture Notes in Bioinformatics, 8701. Berlin ; Heidelberg: Springer Verlag: 174-186.
PUB | DOI
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
Dörr D, Stoye J, Böcker S, Jahn K (2014)
Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings.
BMC Genomics 15(Suppl. 6: Proc. of RECOMB-CG 2014): S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
Lechner M, Hernandez-Rosales M, Dörr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF (2014)
Orthology Detection Combining Clustering and Synteny for Very Large Datasets.
PLoS ONE 9(8): e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D (2014)
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers.
PLOS ONE 9(9): e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Bielefelder E-Dissertation | PUB-ID: 2723541
Ander C (2014)
Bioinformatic methods for the analysis and comparison of metagenomes and metatranscriptomes.
Bielefeld: Universitätsbibliothek Bielefeld.
PUB | PDF
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A (2014)
ReadXplorer - Visualization and Analysis of Mapped Sequences.
Bioinformatics 30(16): 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A (2014)
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Journal of Biotechnology 190: 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014)
Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing.
Journal of Biotechnology 190: 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
Luhmann N, Chauve C, Stoye J, Wittler R (2014)
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
In: Proc. of BSB 2014. Sérgio C (Ed); LNBI, 8826. Springer Verlag: 135-143.
PUB | DOI
 
2014 | Bielefelder E-Dissertation | PUB-ID: 2677466
Hoffmann N (2014)
Computational methods for high-throughput metabolomics.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
Stoye J (2014)
Suffix Tree Construction.
In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag.
PUB | DOI
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691246
Fueller E, Schaefer D, Fischer U, Krell P, Stanulla M, Borkhardt A, Slany RK (2014)
Genomic Inverse PCR for Exploration of Ligated Breakpoints (GIPFEL), a New Method to Detect Translocations in Leukemia.
PloS one 9(8): 104419.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J (2014)
BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry.
Bioinformatics 30(7): 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
Fredrich E, Ander C, Stoye J, Brune I, Tauch A (2014)
Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle.
BIOspektrum 20(5): 294-296.
PUB | DOI
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691732
Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G (2014)
Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria.
Extremophiles 18(5): 853-863.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2691279
Binder V, Bartenhagen C, Okpanyi V, Gombert M, Moehlendick B, Behrens B, Klein H-U, Rieder H, Krell P, Dugas M, Stoecklein NH, Borkhardt A (2014)
A New Workflow for Whole-Genome Sequencing of Single Human Cells.
Human mutation.
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Bielefelder E-Dissertation | PUB-ID: 2673418
Mascher M (2014)
POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U (2014)
Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma.
PLoS ONE 9(3): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
Dias Vieira Braga M, Stoye J (2013)
Restricted DCJ-Indel Model Revisited.
In: Advances in Bioinformatics and Computational Biology. BSB 2013. Setubal JC, Almeida NF (Eds); Lecture Notes in Bioinformatics, 8213. Cham: Springer Verlag: 36-46.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
Willing E, Zaccaria S, Dias Vieira Braga M, Stoye J (2013)
On the Inversion-Indel Distance.
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
Dias Vieira Braga M, Chauve C, Dörr D, Jahn K, Stoye J, Thévenin A, Wittler R (2013)
The Potential of Family-Free Genome Comparison.
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 287-307.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ (2013)
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
BMC Bioinformatics 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2555342
He P, Hao K, Blom J, Rückert C, Vater J, Mao Z, Wu Y, Hou M, He P, He Y, Borriss R (2013)
Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites.
Journal of biotechnology 164(2): 281-291.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Corrigendum: Updating benchtop sequencing performance comparison.
Nature biotechnology 31(12): 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492825
Reuther S, Schmetzer H, Schuster FR, Krell P, Grabrucker C, Liepert A, Kroell T, Kolb H-J, Borkhardt A, Buhmann R (2013)
In vitro-induced response patterns of antileukemic T cells: characterization by spectratyping and immunophenotyping.
Clinical and Experimental Medicine 13(1): 29-48.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
Bergeron A, Stoye J (2013)
The Genesis of the DCJ Formula.
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 63-81.
PUB | DOI
 
2013 | Bielefelder E-Dissertation | PUB-ID: 2604883
Blom J (2013)
Comparative genomics on gene and single nucleotide level.
Bielefeld: Universitätsbibliothek.
PUB | PDF
 
2013 | Bielefelder E-Dissertation | PUB-ID: 2594322
Janowski SJ (2013)
VANESA - A bioinformatics software application for the modeling, visualization, analysis, and simulation of biological networks in systems biology applications.
Bielefeld: Bielefeld University.
PUB | PDF
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
Krell P, Reuther S, Fischer U, Keller T, Weber S, Gombert M, Schuster FR, Asang C, Stepensky P, Strahm B, Meisel R, Stoye J, Borkhardt A (2013)
Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis.
Haematologica 98(9): 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
Gerlach W, Stoye J (2013)
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
In: Encyclopedia of Metagenomics. Nelson KE (Ed); Springer Verlag.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Updating benchtop sequencing performance comparison.
Nature Biotechnology 31(4): 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2625914
Bergmann T, Maeder U, Fiebich M, Dickob M, Nattkemper TW, Anselmetti D (2013)
Categorization of two-photon microscopy images of human cartilage into states of osteoarthritis.
Osteoarthritis And Cartilage 21(8): 1074-1082.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
Darling A, Stoye J (Eds) (2013)
Algorithms in Bioinformatics.
Lecture Notes in Bioinformatics 8126.
PUB | DOI
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn K, Winter S, Stoye J, Böcker S (2013)
Statistics for approximate gene clusters.
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A (2013)
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media.
Journal of Biotechnology 167(2): 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548286
Luque-Almagro VM, Acera F, Igeño MI, Wibberg D, Roldán MD, Sáez LP, Hennig M, Quesada A, Huertas MJ, Blom J, Merchán F, Escribano MP, Jaenicke S, Estepa J, Guijo MI, Martínez-Luque M, Macías D, Szczepanowski R, Becerra G, Ramirez S, Carmona MI, Gutiérrez O, Manso I, Pühler A, Castillo F, Moreno-Vivián C, Schlüter A, Blasco R (2013)
Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.
Environmental Microbiology 15(1): 253-270.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2552092
Wittler R (2013)
Unraveling overlapping deletions by agglomerative clustering.
BMC Genomics 14(Suppl 1): S12.
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529309
Bolzan de Campos S, Youn J-W, Farina R, Jaenicke S, Jünemann S, Szczepanowski R, Beneduzi A, Vargas LK, Wendisch VF, Passaglia L (2013)
Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (*Brassica napus* L. var oleifera) Evaluated through Next-Generation Sequencing.
Microbial Ecology 65(3): 593-601.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659331
Feijão P, Meidanis J (2013)
Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(4): 819-831.
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A (2013)
MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Journal of Biotechnology 167(2): 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2560353
Dörr D, Gronau I, Moran S, Yavneh I (2012)
Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions.
Algorithms for Molecular Biology 7(1): 22.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr D, Thévenin A, Stoye J (2012)
Gene family assignment-free comparative genomics.
BMC Bioinformatics 13(Suppl 19: Proc. of RECOMB-CG 2012): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498160
Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A (2012)
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
BMC Genomics 13(1): 141.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.
BMC Bioinformatics 13(1): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
Jahn K, Sudek H, Stoye J (2012)
Multiple genome comparison based on overlap regions of pairwise local alignments.
BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2513347
Trost E, Blom J, de Castro Soares S, Huang I-H, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata RJ, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A (2012)
Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia.
Journal of bacteriology 194(12): 3199-3215.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490949
Zschuttig A, Zimmermann K, Blom J, Goesmann A, Pohlmann C, Gunzer F (2012)
Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10.
PLoS ONE 7(3): e33351.
PUB | DOI | WoS | PubMed | Europe PMC
 

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