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53 Publikationen

2019 | Bielefelder E-Dissertation | PUB-ID: 2936599
Cloud-based Bioinformatics Framework for Next-Generation Sequencing Data
Huang, Liren, Cloud-based Bioinformatics Framework for Next-Generation Sequencing Data. (). Bielefeld, 2019
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.
Pankoke, Helga, F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota.. FEMS microbiology letters (). , 2019
PUB | DOI | PubMed | Europe PMC
 
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
Nelkner, Johanna, Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes 10 (6). , 2019
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767
CAMISIM: simulating metagenomes and microbial communities
Fritz, Adrian, CAMISIM: simulating metagenomes and microbial communities. Microbiome 7 (). , 2019
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2018 | Bielefelder E-Dissertation | PUB-ID: 2918990
Metadata-driven computational (meta)genomics. A practical machine learning approach
Rumming, Madis, Metadata-driven computational (meta)genomics. A practical machine learning approach. (). Bielefeld, 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts
Celis, Juan Sebastián, Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience 7 (7). , 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Stolze, Yvonne, Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microbial Biotechnology 11 (4). , 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593
Common ELIXIR Service for Researcher Authentication and Authorisation
Linden, Mikael, Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Research 7 (). , 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
AMBER: Assessment of Metagenome BinnERs
Meyer, Fernando, AMBER: Assessment of Metagenome BinnERs. GigaScience (). , 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
Analyzing large scale genomic data on the cloud with Sparkhit
Huang, Liren, Analyzing large scale genomic data on the cloud with Sparkhit. Bioinformatics 34 (9). , 2018
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2018 | Bielefelder Masterarbeit | PUB-ID: 2919932
Concept, design and initial implementation of the de.NBI Cloud Portal
Wiens, Maximilian, Concept, design and initial implementation of the de.NBI Cloud Portal. (). Bielefeld, 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
Maus, Irena, Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels 11 (). , 2018
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea
Fleming, E. J., Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Applied and Environmental Microbiology 84 (9). , 2018
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism
Yu, Jia, Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology 257 (). , 2017
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Bioinformatics for NGS-based metagenomics and the application to biogas research
Jünemann, Sebastian, Bioinformatics for NGS-based metagenomics and the application to biogas research. Journal of Biotechnology 261 (SI). , 2017
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2017 | Datenpublikation | PUB-ID: 2914921
Sparkhit evaluation data set
Huang, Liren, Sparkhit evaluation data set. (). , 2017
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Sczyrba, Alexander, Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods 14 (11). , 2017
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Stolze, Yvonne, Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. Biotechnology for Biofuels 9 (). , 2016
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2016 | Bielefelder E-Dissertation | PUB-ID: 2906743
Assembling the microbial dark matter
Bremges, Andreas, Assembling the microbial dark matter. (). Bielefeld, 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data
Lux, Markus, acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics 17 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type
Heyer, R., Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnology for Biofuels 9 (1). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment
Maus, Irena, Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. Journal of Biotechnology 232 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing
Wibberg, Daniel, Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing. Journal of Biotechnology 232 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering
Stiefel, Fabian, miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering. Journal of Biotechnology 225 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418
Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems
Campos, Samanta B., Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems. Soil Biology and Biochemistry 96 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
Bremges, Andreas, MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics 32 (14). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928
Back to the future of soil metagenomics
Nesme, Joseph, Back to the future of soil metagenomics. Frontiers in Microbiology 7 (). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675
Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.
Krahn, Thomas, Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.. Antimicrobial Agents and Chemotherapy 60 (5). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260
Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates
Maus, Irena, Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnology for Biofuels 9 (1). , 2016
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant
Ortseifen, Vera, An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology 231 (). , 2016
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
Bremges, Andreas, Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience 4 (1). , 2015
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities
Kohrs, Fabian, Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics 15 (20). , 2015
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount
Field, Erin K., Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. The ISME journal 9 (). , 2015
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
Bioboxes: standardised containers for interchangeable bioinformatics software
Belmann, Peter, Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience 4 (). , 2015
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2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612
Automatic discovery of metagenomic structure
Lux, Markus, Automatic discovery of metagenomic structure. 2015 International Joint Conference on Neural Networks (IJCNN) (). , 2015
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
Targeted diversity generation by intraterrestrial archaea and archaeal viruses
Paul, Blair G., Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications 6 (). , 2015
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2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901462
Developing gold standard variant calls for whole-genome somatic variant calling using supervised learning
Rumming, Madis, Developing gold standard variant calls for whole-genome somatic variant calling using supervised learning. (). , 2015
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2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants
Osterholz, Benedikt, A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants. (). , 2015
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling
Piao, Hailan, Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Frontiers in Microbiology 5 (307). , 2014
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features
Kamke, Janine, The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features. PLoS ONE 9 (1). , 2014
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
Ghylin, Trevor W., Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal 8 (12). , 2014
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres
Swan, Brandon K., Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one 9 (4). , 2014
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma
Henrich, Birgit, Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma. PLoS ONE 9 (3). , 2014
PUB | DOI | WoS | PubMed | Europe PMC
 
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344
Wibberg, Daniel, Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Journal of biotechnology 175 (). , 2014
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
Nonlinear dimensionality reduction for cluster identification in metagenomic samples
Gisbrecht, Andrej, Nonlinear dimensionality reduction for cluster identification in metagenomic samples. 17th International Conference on Information Visualisation IV 2013 (). , 2013
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567
Insights into the phylogeny and coding potential of microbial dark matter
Rinke, Christian, Insights into the phylogeny and coding potential of microbial dark matter. Nature 499 (7459). , 2013
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
Campbell, James H., UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences of the United States of America 110 (14). , 2013
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade
Zaremba-Niedzwiedzka, Katarzyna, Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology 14 (11). , 2013
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges
Kamke, Janine, Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME journal 7 (12). , 2013
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543
Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity
Campbell, Alisha G., Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity. PLoS ONE 8 (3). , 2013
PUB | DOI | WoS | PubMed | Europe PMC
 
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean
Swan, Brandon K., Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America 110 (28). , 2013
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Lamprecht, Anna-Lena, GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics 9 (Suppl 4). , 2008
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303
Two interactive bioinformatics courses at the bielefeld university bioinformatics server
Sczyrba, Alexander, Two interactive bioinformatics courses at the bielefeld university bioinformatics server. BRIEFINGS IN BIOINFORMATICS 9 (3). , 2008
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