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414 Publikationen

2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239 OA
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
BMC Bioinformatics 13(1): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644 OA
Multiple genome comparison based on overlap regions of pairwise local alignments
Jahn K, Sudek H, Stoye J (2012)
BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2513347
Pangenomic Study of Corynebacterium diphtheriae That Provides Insights into the Genomic Diversity of Pathogenic Isolates from Cases of Classical Diphtheria, Endocarditis, and Pneumonia
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, et al. (2012)
Journal of bacteriology 194(12): 3199-3215.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490949
Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10
Zschuttig A, Zimmermann K, Blom J, Goesmann A, Pohlmann C, Gunzer F (2012)
PLoS ONE 7(3): e33351.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2709879
Accelerating investigation of food-borne disease outbreaks using pro-active geospatial modeling of food supply chains
Doerr D, Hu K, Renly S, Edlund S, Davis M (2012)
HealthGIS '12: Proceedings of the First ACM SIGSPATIAL International Workshop on Use of GIS in Public Health: 44-47.
PUB | Download (ext.)
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2527519
Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications
Ruijter JM, Pfaffl MW, Zhao S, Spiess AN, Boggy G, Blom J, Rutledge RG, Sisti D, Lievens A, De Preter K, Derveaux S, et al. (2012)
Methods. A companion to methods in enzymology (San Diego, Calif.) 59(1): 32-46.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553484
Probabilistic Arithmetic Automata and Their Applications
Marschall T, Herms I, Kaltenbach H-M, Rahmann S (2012)
Ieee/Acm Transactions On Computational Biology And Bioinformatics 9(6): 1737-1750.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2468026 OA
Taxonomic classification of metagenomic sequences
Gerlach W (2012)
Bielefeld: Universität.
PUB | PDF
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553300
Linearization of ancestral multichromosomal genomes
Manuch J, Patterson M, Wittler R, Chauve C, Tannier E (2012)
BMC Bioinformatics 13(Proc. of RECOMB-CG 2012).
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659289
Genome Sequence and Assembly of Bos indicus
Canavez FC, Luche DD, Stothard P, Leite KRM, Sousa-Canavez JM, Plastow G, Meidanis J, Souza MA, Feijão P, Moore SS, Camara-Lopes LH (2012)
Journal of Heredity 103(3): 342-348.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659385
A GRASP-based Heuristic for the Project Portfolio Selection Problem
Mira C, Feijão P, Souza MA, Moura A, Meidanis J, Lima G, Schmitz R, Bossolan RP, Freitas IT (2012)
In: 2012 IEEE 15th International Conference on Computational Science and Engineering. 36-41.
PUB | DOI | WoS
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553455
The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification
De Maayer P, Chan W-Y, Blom J, Venter SN, Duffy B, Smits THM, Coutinho TA (2012)
Bmc Genomics 13(1): 625.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060 OA
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110
Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A (2012)
BMC Genomics 13(1): 112.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659280
Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation.
Biller P, Feijão P, Meidanis J (2012)
IEEE/ACM transactions on computational biology and bioinformatics 10(1): 122-134.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
Combinatorial Pattern Matching
Kärkkäinen J, Stoye J (Eds) (2012)
Lecture Notes in Computer Science 7354.
PUB | DOI
 
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382 OA
Generic Software Frameworks for GC-MS Based Metabolomics
Hoffmann N, Stoye J (2012)
In: Metabolomics. Roessner U (Ed); InTech: 73-98.
PUB | PDF | DOI | Download (ext.)
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ
Hilker R, Sickinger C, Pedersen CNS, Stoye J (2012)
Bioinformatics 28(19): 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2542210 PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2533144 OA PUB | PDF
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2493233
ALGORITHMS FOR JUMBLED PATTERN MATCHING IN STRINGS
Burcsi P, Cicalese F, Fici G, Lipták Z (2012)
International Journal of Foundations of Computer Science 23(02): 357-374.
PUB | DOI | WoS | arXiv
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2517237 OA PUB | PDF
 
2012 | Bielefelder E-Dissertation | PUB-ID: 2484427 OA PUB | PDF
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526281
Complete Genome Sequence of the Porcine Isolate Enterococcus faecalis D32
Zischka M, Kuenne C, Blom J, Dabrowski PW, Linke B, Hain T, Nitsche A, Goesmann A, Larsen J, Jensen LB, Witte W, et al. (2012)
Journal of Bacteriology 194(19): 5490-5491.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526298
Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, et al. (2012)
Journal of Bacteriology 194(19): 5487-5488.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2526933
Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties
Dohrmann AB, Küting M, Jünemann S, Jaenicke S, Schlüter A, Tebbe CC (2012)
The ISME journal 7(1): 37-49.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing
Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D (2012)
PLoS ONE 7(8): e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2501312
Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting
Gorzolka K, Lissel M, Kessler N, Loch-Ahring S, Niehaus K (2012)
Journal of Biotechnology 159(3): 177-187.
PUB | DOI | WoS | PubMed | Europe PMC
 
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2490286
Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information
Vogel U, Szczepanowski R, Claus H, Jünemann S, Prior K, Harmsen D (2012)
Journal of clinical microbiology 50(6): 1889-1894.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558 OA
On the weight of indels in genomic distances
Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: RECOMB-CG 2011): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509 OA
Genomic distance under gene substitutions
Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
Double Cut and Join with Insertions and Deletions
Dias Vieira Braga M, Willing E, Stoye J (2011)
Journal of Computational Biology 18(9): 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation
Kovac J, Warren R, Dias Vieira Braga M, Stoye J (2011)
Journal of Computational Biology 18(9): 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology
Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A (2011)
Journal of Biotechnology 155(1): 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375634
The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis
Pothier JF, Vorhölter F-J, Blom J, Goesmann A, Pühler A, Smits TH, Duffy B (2011)
FEMS Microbiology Letters 323(1): 52-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2404767 PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354731
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid
Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Szczepanowski R, Goesmann A, Setubal JC, Schmitt R, et al. (2011)
Journal of Biotechnology 155(1): 50-62.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659339
SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems
Feijão P, Meidanis J (2011)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(5): 1318-1329.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326511
Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42
Rückert C, Blom J, Chen XH, Reva O, Borriss R (2011)
Journal of Biotechnology 155(1): 78-85.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2373808
Multivariate Image Mining
Herold J, Loyek C, Nattkemper TW (2011)
Wiley Interdisciplinary Reviews: DATA MINING AND KNOWLEDGE DISCOVERY 1(1): 2-13.
PUB | DOI | WoS
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2659373
The SinBiota 2.0 Biodiversity Information System
Mira C, Feijão P, Duque-Estrada T, Meidanis J, Joly CA (2011)
In: 2011 IEEE Seventh International Conference on eScience. 142-149.
PUB | DOI
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2401639
On prefix normal words
Fici G, Lipták Z (2011)
In: Development in Language Theory. 15th International Conference (DLT 2011). Proceedings. Mauri G, Leporati A (Eds); Lecture Notes in Computer Science, 6795. Berlin ; Heidelberg: Springer: 228-238.
PUB | DOI
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2401665
KABOOM! A new suffix-array based algorithm for clustering expression data
Hazelhurst S, Lipták Z (2011)
Bioinformatics 27(24): 3348-3355.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2375954 PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2472468
Erwinia amylovora novel plasmid pEI70: Complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen
Llop P, Cabrefiga J, Smits THM, Dreo T, Barbé S, Pulawska J, Bultreys A, Blom J, Duffy B, Montesinos E, Lopez MM (2011)
PLoS one 6(12): e28651.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2423955
Efficient Reconstruction of RC-Equivalent Strings
Cicalese F, Erdős PLP, Lipták Z (2011)
In: Proc. WOCA., 6460. 349-362.
PUB | DOI
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326445
RAPYD - Rapid Annotation Platform for Yeast Data
Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A (2011)
Journal of Biotechnology 155(1): 118-126.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2307104
Metabolic Versatility and Antibacterial Metabolite Biosynthesis Are Distinguishing Genomic Features of the Fire Blight Antagonist Pantoea vagans C9-1
Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B (2011)
PLoS ONE 6(7): e22247.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2448409
The genomics of Acinetobacter baumannii: Insights into genome plasticity, antimicrobial resistance and pathogenicity
Imperi F, Antunes L, Blom J, Villa L, Iacono M, Visca P, Carattoli A (2011)
IUBMB life 63(12): 1068-1074.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326455
RhizoRegNet-A database of rhizobial transcription factors and regulatory networks
Krol E, Blom J, Winnebald J, Berhoerster A, Barnett MJ, Goesmann A, Baumbach J, Becker A (2011)
Journal of Biotechnology 155(1): 127-134.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2326518
Sequencing and comparative analysis of IncP-1 alpha antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions
Szczepanowski R, Eikmeyer FG, Harfmann J, Blom J, Rogers LM, Top EM, Schlüter A (2011)
Journal of Biotechnology 155(1): 95-103.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2329973
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes
Wittler R, Chauve C (2011)
BMC Bioinformatics 12(Suppl. 9): S21.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425344
Efficient Reconstruction of RC-Equivalent Strings
Cicalese F, Erdős PLP, Lipták Z (2011)
In: Combinatorial Algorithms : 21st International Workshop, IWOCA 2010, London, UK, July 26-28, 2010, Revised Selected Papers. Lecture Notes in Computer Science, 6460. Berlin, Heidelberg: Springer: 349-362.
PUB | DOI
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2290032
Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome
Joseph B, Schwarz RF, Linke B, Blom J, Becker A, Claus H, Goesmann A, Frosch M, Mueller T, Vogel U, Schoen C (2011)
PLoS ONE 6(4): e18441.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093389
Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594
Schoen C, Weber-Lehmann J, Blom J, Joseph B, Goesmann A, Strittmatter A, Frosch M (2011)
Journal of Bacteriology 193(8): 2064-2065.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2289887
Complete Genome Analysis of Streptococcus gallolyticus subsp gallolyticus, an Emerging Pathogen of Infective Endocarditis
Hinse D, Vollmer T, Rückert C, Blom J, Kalinowski J, Knabbe C, Dreier J (2011)
Clinical Chemistry and Laboratory Medicine 49: S837.
PUB | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011)
Bioinformatics 27(10): 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Bielefelder E-Dissertation | PUB-ID: 2324501 OA
Bioinformatic approaches for genome finishing
Husemann P, Tauch A (2011)
Bielefeld: Universitätsbibliothek Bielefeld.
PUB | PDF
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425310
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling
Wolfsheimer S, Herms I, Rahmann S, Hartmann AK (2011)
BMC Bioinformatics 12(1): 47-2105.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310613
Tractability results for the Consecutive-Ones Property with multiplicity
Chauve C, Maňuch J, Patterson M, Wittler R (2011)
In: Proceedings of CPM 2011., 6661. 90-103.
PUB | DOI | Download (ext.)
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289928
Comparative genomics of Lactobacillus
Kant R, Blom J, Palva A, Siezen RJ, de Vos WM (2011)
Microbial Biotechnology 4(3): 323-332.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2492807
Highly skewed T-cell receptor V-beta chain repertoire in the bone marrow is associated with response to immunosuppressive drug therapy in children with very severe aplastic anemia
Schuster FR, Hubner B, Führer M, Eckermann O, Gombert M, Dornmair K, Binder V, Reuther S, Krell P, Keller T, Borkhardt A (2011)
Blood Cancer Journal 1(3): e8.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2017892
The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome
Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorhölter F-J, Weidner S, Goesmann A, Pühler A, et al. (In Press)
Journal of Biotechnology 155(1): 20-33.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
Common Intervals of Multiple Permutations
Heber S, Mayr R, Stoye J (2011)
Algorithmica 60(2): 175-206.
PUB | DOI | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2087955
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering
Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner zu Siederdissen C, Bort JAH, Wieser M, Kunert R, et al. (2011)
Journal of Biotechnology 153(1-2): 62-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2036058
Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean
Margaret I, Becker A, Blom J, Bonilla I, Goesmann A, Göttfert M, Lloret J, Mittard-Runte V, Rückert C, Ruiz-Sainz J-E, Vinardell JM, et al. (2011)
Journal of Biotechnology 155(1): 11-19.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170 OA
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J (2011)
Nucleic Acids Res 39(14): e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2003418
Genome Sequence of an Erwinia amylovora Strain with Pathogenicity Restricted to Rubus Plants
Powney R, Smits THM, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B (2011)
Journal of Bacteriology 193(3): 785-786.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance
Erdős PL, Soukup L, Stoye J (2011)
Applied Mathematics Letters 24(1): 82-86.
PUB | DOI | WoS
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
Consistency of Sequence-Based Gene Clusters
Wittler R, Maňuch J, Patterson M, Stoye J (2011)
Journal of Computational Biology 18(9): 1023-1039.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093398
Genome of a European Fresh-Vegetable Food Safety Outbreak Strain of Salmonella enterica subsp enterica Serovar Weltevreden
Brankatschk K, Blom J, Goesmann A, Smits THM, Duffy B (2011)
Journal of Bacteriology 193(8): 2066.
PUB | DOI | WoS | PubMed | Europe PMC
 
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2011)
BMC Bioinformatics 12(1): 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301939 OA
Phylogeny-based analysis of gene clusters
Wittler R (2010)
Bielefeld (Germany): Bielefeld University.
PUB | PDF | Download (ext.)
 
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2907492
A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2010)
In: Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L (Eds); Dagstuhl Seminar Proceedings, 10231. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany.
PUB | Download (ext.)
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2303705 OA
Approximate common intervals based gene cluster models
Jahn K (2010)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2301975 OA
Clustering biological data by unraveling hidden transitive substructures
Wittkop T (2010)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2308298
One-year time series of investigations of analytes within human breath using ion mobility spectrometry
Bunkowski A, Maddula S, Davies AN, Westhoff M, Litterst P, Bödeker B, Baumbach JI (2010)
Int. J. Ion Mobility Spectrometry 13(3-4): 141-148.
PUB | DOI | Download (ext.)
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425329
Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS
Bunkowski A (2010)
Int. J. Ion Mobil. Spectrom. 13(3-4): 169-175.
PUB | DOI
 
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
Computing the Genomic Distance in Linear Time
Bergeron A, Mixtacki J, Stoye J (2010)
In: Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L (Eds); , 10231. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 18.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1929692
CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks
Schneider J, Vorhölter F-J, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A (2010)
Genetics and Molecular Research 9(3): 1660-1672.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425332
On Table Arrangements, Scrabble Freaks, and Jumbled Pattern Matching
Burcsi P, Cicalese F, Fici G, Lipták Z (2010)
In: Fun with Algorithms: 5th International Conference, FUN 2010, Ischia, Italy, June 2-4, 2010. Proceedings. Boldi P (Ed); Lecture Notes in Computer Science, 6099. Berlin, Heidelberg: Springer: 89-101.
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2425351 PUB
 
2010 | Bielefelder E-Dissertation | PUB-ID: 2302499 OA
Biological applications for de Bruijn subgraphs and interval group testing
Quitzau JAA (2010)
Bielefeld (Germany): Bielefeld University.
PUB | PDF
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893 OA
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2010)
Algorithms for Molecular Biology 5(1): 3.
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2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
Indexing and Searching a Mass Spectrometry Database
Besenbacher S, Schwikowski B, Stoye J (2010)
In: Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Elomaa T, Mannila H, Orponen P (Eds); LNCS, 6060. 62-76.
PUB | DOI
 
2010 | Report | Veröffentlicht | PUB-ID: 1966434 PUB | arXiv
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence
Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Alves Dorella F, Souza Rocha F, de Castro Soares S, et al. (2010)
BMC Genomics 11(1): 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785275 OA
Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion
Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehöver P, Arnold W, Bekel T, Blom J, Gartemann K-H, et al. (2010)
BMC Genomics 11(1): 91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
Partitioning Biological Data with Transitivity Clustering
Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010)
Nature Methods 7(6): 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1796445
Complete Genome Sequence of the Fire Blight Pathogen Erwinia amylovora CFBP 1430 and Comparison to Other Erwinia spp.
Smits THM, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B (2010)
MOLECULAR PLANT-MICROBE INTERACTIONS 23(4): 384-393.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
Finding Nested Common Intervals Efficiently
Blin G, Faye D, Stoye J (2010)
Journal of Computational Biology 17(9): 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1894907
Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions
Mittard-Runte V, Bekel T, Blom J, Dondrup M, Henckel K, Jaenicke S, Krause L, Linke B, Neuweger H, Schneiker-Bekel S, Goesmann A (2010)
In: Introduction to Marine Genomics (Advances in Marine Genomics). Cock JM, Tessmar-Raible K, Boyen C, Viard F (Eds); , 1. Netherlands: Springer Netherlands: 315-396.
PUB | DOI
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
Consistency of Sequence-based Gene Clusters
Wittler R, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. Springer Verlag: 252-263.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
Repeat-aware Comparative Genome Assembly
Husemann P, Stoye J (2010)
In: Proc. of GCB 2010. LNI, P-173. 61-70.
PUB | Download (ext.)
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
r2cat: Synteny Plots and Comparative Assembly
Husemann P, Stoye J (2010)
Bioinformatics 26(4): 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
Rearrangement Models and Single-Cut Operations
Bergeron A, Medvedev P, Stoye J (2010)
Journal of Computational Biology 17(9): 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2010)
In: Proc. of WABI 2010. LNBI, 6293. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving
Kovac J, Dias Vieira Braga M, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. 13-24.
PUB | DOI
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1794419
Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue
Herold J, Zhou L, Abouna S, Pelengaris S, Epstein D, Khan M, Nattkemper TW (2010)
Computerized Medical Imaging and Graphics 34(6): 446-452.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
The Solution Space of Sorting by DCJ
Dias Vieira Braga M, Stoye J (2010)
Journal of Computational Biology 17(9): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
Genomic Distance with DCJ and Indels
Dias Vieira Braga M, Willing E, Stoye J (2010)
In: Proc. of WABI 2010. LNBI, 6293. 90-101.
PUB | DOI
 

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