Please note that PUB no longer supports Internet Explorer versions 8 or 9 (or earlier).

We recommend upgrading to the latest Internet Explorer, Google Chrome, or Firefox.

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
 

Filter und Suchbegriffe

department=66100

Suche

Publikationen filtern

Darstellung / Sortierung

Zitationsstil: bio1

Export / Einbettung