76 Publikationen

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[76]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223
Belmann, Peter, Fischer, Björn, Krüger, Jan, Procházka, Michal, Rasche, Helena, Prinz, Manuel, Hanussek, Maximilian, Lang, Martin, Bartusch, Felix, Gläßle, Benjamin, Krüger, Jens, Pühler, Alfred, and Sczyrba, Alexander. “de.NBI Cloud federation through ELIXIR AAI”. F1000Research 8 (2019): 842.
PUB | PDF | DOI | PubMed | Europe PMC
 
[75]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
Pankoke, Helga, Maus, Irena, Loh, Gunnar, Huser, Andrea, Seifert, Jana, Tilker, Alexandra, Hark, Sarah, Sczyrba, Alexander, Pelzer, Stefan, and Kleinbolting, Jessica. “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
 
[74]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
Nelkner, Johanna, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “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): 424.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[73]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767
Fritz, Adrian, Hofmann, Peter, Majda, Stephan, Dahms, Eik, Dröge, Johannes, Fiedler, Jessika, Lesker, Till R., Belmann, Peter, DeMaere, Matthew Z., Darling, Aaron E., Sczyrba, Alexander, Bremges, Andreas, and McHardy, Alice C. “CAMISIM: simulating metagenomes and microbial communities”. Microbiome 7 (2019): 17.
PUB | DOI | WoS | PubMed | Europe PMC
 
[72]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants”. Microbial Biotechnology 11.4 (2018): 667-679.
PUB | DOI | WoS | PubMed | Europe PMC
 
[71]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, and Wilke, Thomas. “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”. GigaScience 7.7 (2018): giy075.
PUB | DOI | WoS | PubMed | Europe PMC
 
[70]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, and McHardy, Alice C. “AMBER: Assessment of Metagenome BinnERs”. GigaScience (2018): giy069.
PUB | DOI | WoS | PubMed | Europe PMC
 
[69]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593
Linden, Mikael, Prochazka, Michal, Lappalainen, Ilkka, Bucik, Dominik, Vyskocil, Pavel, Kuba, Martin, Silén, Sami, Belmann, Peter, Sczyrba, Alexander, Newhouse, Steven, Matyska, Ludek, and Nyrönen, Tommi. “Common ELIXIR Service for Researcher Authentication and Authorisation”. F1000Research 7 (2018): 1199.
PUB | DOI | Download (ext.) | PubMed | Europe PMC
 
[68]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. “Analyzing large scale genomic data on the cloud with Sparkhit”. Bioinformatics 34.9 (2018): 1457-1465.
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750
Maus, Irena, Rumming, Madis, Bergmann, Ingo, Heeg, Kathrin, Pohl, Marcel, Nettmann, Edith, Jaenicke, Sebastian, Blom, Jochen, Pühler, Alfred, Schlüter, Andreas, Sczyrba, Alexander, and Klocke, Michael. “Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors”. Biotechnology for Biofuels 11 (2018): 167.
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, Alexander, Littmann, S., and Emerson, D. “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”. Applied and Environmental Microbiology 84.9 (2018): e02239-17.
PUB | DOI | WoS | PubMed | Europe PMC
 
[65]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914959
da Schoren Costa, Pedro, Bolzan de Campos, Samanta, Albersmeier, Andreas, Dirksen, Paul, Pereira Dresseno, André Luis, Andrade Pais dos Santos, Odair José, Lima Milani, Karina Maria, Etto, Rafael Mazer, Battistus, André Gustavo, Peres Rodrigues da Costa, Andréia Cristina, Martinez de Oliveira, André Luiz, Weigert Galvão, Carolina, Guimarães, Vandeir Francisco, Sczyrba, Alexander, Wendisch, Volker F., and Passaglia, Luciane. “Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach”. Plant and Soil 422.1-2 (2018): 467-478.
PUB | DOI | WoS
 
[64]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
Yu, Jia, Blom, Jochen, Sczyrba, Alexander, and Goesmann, Alexander. “Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism”. Journal of Biotechnology 257 (2017): 58-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
[63]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, Albaum, Stefan, Schlüter, Andreas, Goesmann, Alexander, Sczyrba, Alexander, and Stoye, Jens. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261.SI (2017): 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[62]
2017 | Datenpublikation | PUB-ID: 2914921
Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. Sparkhit evaluation data set. Bielefeld University, 2017.
PUB | Dateien verfügbar | DOI
 
[61]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G., Koeck, Daniela E., Kim, Yong S., Kreubel, Jana, Hassa, Julia, Wibberg, Daniel, Weimann, Aaron, Off, Sandra, Stantscheff, Robbin, Zverlov, Vladimir V., Schwarz, Wolfgang H., König, Helmut, Liebl, Wolfgang, Scherer, Paul, McHardy, Alice C., Sczyrba, Alexander, Klocke, Michael, Pühler, Alfred, and Schlüter, Andreas. “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”. Biotechnology for Biofuels 10.1 (2017): 264.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiūtė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton K H, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, and McHardy, Alice C. “Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software”. Nature Methods 14.11 (2017): 1063-1071.
PUB | DOI | WoS | PubMed | Europe PMC
 
[59]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “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): 156.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
Lux, Markus, Krüger, Jan, Rinke, Christian, Maus, Irena, Schlüter, Andreas, Woyke, Tanja, Sczyrba, Alexander, and Hammer, Barbara. “acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data”. BMC Bioinformatics 17 (2016): 543.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836
Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E., Schlüter, Andreas, Sczyrba, Alexander, and Reichl, U. “Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type”. Biotechnology for Biofuels 9.1 (2016): 155.
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
Maus, Irena, Cibis, Katharina Gabriela, Bremges, Andreas, Stolze, Yvonne, Wibberg, Daniel, Tomazetto, Geizecler, Blom, Jochen, Sczyrba, Alexander, König, Helmut, Pühler, Alfred, and Schlüter, Andreas. “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): 50-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
[55]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
Wibberg, Daniel, Bremges, Andreas, Dammann-Kalinowski, Tanja, Maus, Irena, Igeño, Maria Isabel, Vogelsang, Ralph, König, Christoph, Luque-Almagro, Víctor M., Roldán, Maria Dolores, Sczyrba, Alexander, Moreno-Vivián, Conrado, Blasco, Rafael, Pühler, Alfred, and Schlüter, Andreas. “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): 61-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
[54]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418
Campos, Samanta B., Lisboa, Bruno B., Camargo, Flavio A.O., Bayer, Cimelio, Sczyrba, Alexander, Dirksen, Paul, Albersmeier, Andreas, Kalinowski, Jörn, Beneduzi, Anelise, Costa, Pedro B., Passaglia, Luciane Maria P., Vargas, Luciano K., and Wendisch, Volker F. “Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems”. Soil Biology and Biochemistry 96 (2016): 191-197.
PUB | DOI | WoS
 
[53]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
Stiefel, Fabian, Fischer, Simon, Sczyrba, Alexander, Otte, Kerstin, and Hesse, Friedemann. “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): 31-43.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
Bremges, Andreas, Singer, Esther, Woyke, Tanja, and Sczyrba, Alexander. “MeCorS: Metagenome-enabled error correction of single cell sequencing reads”. Bioinformatics 32.14 (2016): 2199-2201.
PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675
Krahn, Thomas, Wibberg, Daniel, Maus, Irena, Winkler, Anika, Bontron, Séverine, Sczyrba, Alexander, Nordmann, Patrice, Pühler, Alfred, Poirel, Laurent, and Schlüter, Andreas. “Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.”. Antimicrobial Agents and Chemotherapy 60.5 (2016): 3032-3040.
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928
Nesme, Joseph, Achouak, Wafa, Agathos, Spiros, Bailey, Mark, Baldrian, Petr, Brunel, Dominique, Frostegard, Asa, Heulin, Thierry, Jansson, Janet K., Jurkevitch, Edouard, Kowalchuk, George A., Kruus, Kristiina Leena, Lagares, Antonio, Lapin-Scott, Hilary M., Le Paslier, Denis, ic-Mulec, Ines, Murrell, Colin, Myrold, David D., Nalin, Renaud, Nannipieri, Paolo, Neufeld, Josh David, O'Gara, Fergal, Parnell, John Jacob, Pühler, Alfred, Pylro, Victor, Ramos, Juan Luis, Roesch, Luiz, Schleper, Christa, Schloter, Michael, Sczyrba, Alexander, Sessitsch, Angela, Sjöling, Sara, Sørensen, Jan, Sørensen, Søren J, Tebbe, Christoph C., Topp, Ed, Tsiamis, George, Van Elsas, Jan Dirk, Van Keulen, Geertje, Wagner, Michael, Widmer, Franco, Zhang, Tong, Zhang, Xiaojun, Zhao, Liping, Zhu, Yong-Guan, Vogel, Timothy M., and Simonet, Pascal. “Back to the future of soil metagenomics”. Frontiers in Microbiology 7 (2016): 73.
PUB | DOI | WoS | PubMed | Europe PMC
 
[49]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260
Maus, Irena, Koeck, Daniela E., Cibis, Katharina G., Hahnke, Sarah, Kim, Yong S., Langer, Thomas, Kreubel, Jana, Erhard, Marcel, Bremges, Andreas, Off, Sandra, Stolze, Yvonne, Jaenicke, Sebastian, Goesmann, Alexander, Sczyrba, Alexander, Scherer, Paul, König, Helmut, Schwarz, Wolfgang H., Zverlov, Vladimir V., Liebl, Wolfgang, Pühler, Alfred, Schlüter, Andreas, and Klocke, Michael. “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): 171.
PUB | DOI | WoS | PubMed | Europe PMC
 
[48]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan, Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, and Schlüter, Andreas. “An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant”. Journal of Biotechnology 231 (2016): 268-279.
PUB | DOI | WoS | PubMed | Europe PMC
 
[47]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
Bremges, Andreas, Maus, Irena, Belmann, Peter, Eikmeyer, Felix Gregor, Winkler, Anika, Albersmeier, Andreas, Pühler, Alfred, Schlüter, Andreas, and Sczyrba, Alexander. “Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant”. GigaScience 4.1 (2015): 33.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, and Reichl, Udo. “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”. Proteomics 15.20 (2015): 3585-3589.
PUB | DOI | WoS | PubMed | Europe PMC
 
[45]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
Field, Erin K., Sczyrba, Alexander, Lyman, Audrey E., Harris, Christopher C., Woyke, Tanja, Stepanauskas, Ramunas, and Emerson, David. “Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount”. The ISME journal 9 (2015): 857-870.
PUB | DOI | WoS | PubMed | Europe PMC
 
[44]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C, Sczyrba, Alexander, and Barton, Michael D. “Bioboxes: standardised containers for interchangeable bioinformatics software”. GigaScience 4 (2015): 47.
PUB | DOI | WoS | PubMed | Europe PMC
 
[43]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612
Lux, Markus, Sczyrba, Alexander, and Hammer, Barbara. “Automatic discovery of metagenomic structure”. 2015 International Joint Conference on Neural Networks (IJCNN). Institute of Electrical & Electronics Engineers (IEEE), 2015.
PUB | DOI
 
[42]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
Paul, Blair G., Bagby, Sarah C., Czornyj, Elizabeth, Arambula, Diego, Handa, Sumit, Sczyrba, Alexander, Ghosh, Partho, Miller, Jeff F., and Valentine, David L. “Targeted diversity generation by intraterrestrial archaea and archaeal viruses”. Nature Communications 6 (2015): 6585.
PUB | DOI | WoS | PubMed | Europe PMC
 
[41]
2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
Osterholz, Benedikt, Wiebke, Pätzold, Fust, Annika, Rumming, Madis, Schlüter, Andreas, and Sczyrba, Alexander. “A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants”. Presented at the 3rd International Symposium on the environmental Dimension of Antibiotic Resistance, Wernigerode, 2015.
PUB
 
[40]
2015 | Report | Veröffentlicht | PUB-ID: 2901613
Lux, Markus, Hammer, Barbara, and Sczyrba, Alexander. Automated Contamination Detection in Single-Cell Sequencing. Cold Spring Harbor Laboratory Press, 2015.
PUB | DOI
 
[39]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
Piao, Hailan, Lachman, Medora, Malfatti, Stephanie, Sczyrba, Alexander, Knierim, Bernhard, Auer, Manfred, Tringe, Susannah Green, Mackie, Roderick Ian, Yeoman, Carl James, and Hess, Matthias. “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).
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[38]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
Kamke, Janine, Rinke, Christian, Schwientek, Patrick, Mavromatis, Kostas, Ivanova, Natalia, Sczyrba, Alexander, Woyke, Tanja, and Hentschel, Ute. “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): e87353.
PUB | DOI | WoS | PubMed | Europe PMC
 
[37]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051
Ghylin, Trevor W., Garcia, Sarahi L., Moya, Francisco, Oyserman, Ben O., Schwientek, Patrick, Forest, Katrina T., Mutschler, James, Dwulit-Smith, Jeffrey, Chan, Leong-Keat, Martinez-Garcia, Manuel, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, Warnecke, Falk, Malmstrom, Rex, Bertilsson, Stefan, and McMahon, Katherine D. “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”. The ISME Journal 8.12 (2014): 2503-2516.
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163
Heins, Richard A, Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P, Chivian, Dylan C, Datta, Supratim, Friedland, Gregory D, D'Haeseleer, Patrik, Wu, Dongying, Tran-Gyamfi, Mary, Scullin, Chessa S, Singh, Seema, Shi, Weibing, Hamilton, Matthew G, Bendall, Matthew L, Sczyrba, Alexander, Thompson, John, Feldman, Taya, Guenther, Joel M, Gladden, John M, Cheng, Jan-Fang, Adams, Paul D, Rubin, Edward M, Simmons, Blake A, Sale, Kenneth L, Northen, Trent R, and Deutsch, Samuel. “Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry”. ACS chemical biology 9.9 (2014): 2082-2091.
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
Swan, Brandon K., Chaffin, Mark D., Martinez-Garcia, Manuel, Morrison, Hilary G., Field, Erin K., Poulton, Nicole J., Masland, E. Dashiell P., Harris, Christopher C., Sczyrba, Alexander, Chain, Patrick S. G., Koren, Sergey, Woyke, Tanja, and Stepanauskas, Ramunas. “Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres”. PloS one 9.4 (2014): 95380.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, Rahn, Sebastian, Stoye, Jens, Borkhardt, Arndt, and Fischer, Ute. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9.3 (2014): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[33]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
Wibberg, Daniel, Luque-Almagro, Víctor M., Igeño, M. Isabel, Bremges, Andreas, Roldán, M. Dolores, Merchán, Faustino, Sáez, Lara P., Guijo, M. Isabel, Manso, M. Isabel, Macías, Daniel, Cabello, Purificación, Becerra, Gracia, Ibáñez, M. Isabel, Carmona, M. Isabel, Escribano, M. Paz, Castillo, Francisco, Sczyrba, Alexander, Moreno-Vivián, Conrado, Blasco, Rafael, Pühler, Alfred, and Schlüter, Andreas. “Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344”. Journal of biotechnology 175 (2014): 67-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
[32]
2013 | Konferenzbeitrag | PUB-ID: 2909357
Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. IV. 2013. 174-179.
PUB
 
[31]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. 17th International Conference on Information Visualisation IV 2013. Ed. Ebad Banissi. 2013. 174-179.
PUB
 
[30]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N, Anderson, Iain J, Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K, Gies, Esther A, Dodsworth, Jeremy A, Hedlund, Brian P, Tsiamis, George, Sievert, Stefan M, Liu, Wen-Tso, Eisen, Jonathan A, Hallam, Steven J, Kyrpides, Nikos C, Stepanauskas, Ramunas, Rubin, Edward M, Hugenholtz, Philip, and Woyke, Tanja. “Insights into the phylogeny and coding potential of microbial dark matter”. Nature 499.7459 (2013): 431-437.
PUB | DOI | WoS | PubMed | Europe PMC
 
[29]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
Campbell, James H., O'Donoghue, Patrick, Campbell, Alisha G., Schwientek, Patrick, Sczyrba, Alexander, Woyke, Tanja, Söll, Dieter, and Podar, Mircea. “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): 5540-5545.
PUB | DOI | WoS | PubMed | Europe PMC
 
[28]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
Zaremba-Niedzwiedzka, Katarzyna, Viklund, Johan, Zhao, Weizhou, Ast, Jennifer, Sczyrba, Alexander, Woyke, Tanja, McMahon, Katherina, Bertilsson, Stefan, Stepanauskas, Ramunas, and Andersson, Siv Ge. “Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade”. Genome biology 14.11 (2013): R130.
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
Kamke, Janine, Sczyrba, Alexander, Ivanova, Natalia, Schwientek, Patrick, Rinke, Christian, Mavromatis, Kostas, Woyke, Tanja, and Hentschel, Ute. “Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges”. The ISME journal 7.12 (2013): 2287-2300.
PUB | DOI | WoS | PubMed | Europe PMC
 
[26]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543
Campbell, Alisha G., Campbell, James H., Schwientek, Patrick, Woyke, Tanja, Sczyrba, Alexander, Allman, Steve, Beall, Clifford J., Griffen, Ann, Leys, Eugene, and Podar, Mircea. “Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity”. PLoS ONE 8.3 (2013): e59361.
PUB | DOI | WoS | PubMed | Europe PMC
 
[25]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623
Swan, Brandon K., Tupper, Ben, Sczyrba, Alexander, Lauro, Federico M., Martinez-Garcia, Manuel, González, José M., Luo, Haiwei, Wright, Jody J., Landry, Zachary C., Hanson, Niels W., Thompson, Brian P., Poulton, Nicole J., Schwientek, Patrick, Acinas, Silvia G., Giovannoni, Stephen J., Moran, Mary Ann, Hallam, Steven J., Cavicchioli, Ricardo, Woyke, Tanja, and Stepanauskas, Ramunas. “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): 11463-11468.
PUB | DOI | WoS | PubMed | Europe PMC
 
[24]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2518330
Garcia, Sarahi L, McMahon, Katherine D, Martinez-Garcia, Manuel, Srivastava, Abhishek, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, and Warnecke, Falk. “Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton”. The ISME journal 7.1 (2012): 137-147.
PUB | DOI | WoS | PubMed | Europe PMC
 
[23]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307
El-Kalioby, Mohamed, Abouelhoda, Mohamed, Krüger, Jan, Giegerich, Robert, Sczyrba, Alexander, Wall, Dennis P, and Tonellato, Peter. “Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package”. BMC Bioinformatics 13.Suppl 17 (2012): S22.
PUB | DOI | WoS | PubMed | Europe PMC
 
[22]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2329885
Swan, Brandon K., Martinez-Garcia, Manuel, Preston, Christina M., Sczyrba, Alexander, Woyke, Tanja, Lamy, Dominique, Reinthaler, Thomas, Poulton, Nicole J., Masland, E. Dashiell P., Gomez, Monica Lluesma, Sieracki, Michael E., DeLong, Edward F., Herndl, Gerhard J., and Stepanauskas, Ramunas. “Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean”. Science 333.6047 (2011): 1296-1300.
PUB | DOI | WoS | PubMed | Europe PMC
 
[21]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2351462
Kim, Tae-Wan, Chokhawala, Harshal A., Hess, Matthias, Dana, Craig M., Baer, Zachary, Sczyrba, Alexander, Rubin, Edward M., Blanch, Harvey W., and Clark, Douglas S. “High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery”. Angewandte Chemie 123.47 (2011): 11411-11414.
PUB | DOI | PubMed | Europe PMC
 
[20]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2789582
Sales, Christopher M., Mahendra, Shaily, Grostern, Ariel, Parales, Rebecca E, Goodwin, Lynne A, Woyke, Tanja, Nolan, Matt, Lapidus, Alla, Chertkov, Olga, Ovchinnikova, Galina, Sczyrba, Alexander, and Alvarez-Cohen, Lisa. “Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190”. Journal of Bacteriology 193.17 (2011): 4549-4550.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
 
[19]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410148
Woyke, Tanja, Sczyrba, Alexander, Lee, Janey, Rinke, Christian, Tighe, Damon, Clingenpeel, Scott, Malmstrom, Rex, Stepanauskas, Ramunas, and Cheng, Jan-Fang. “Decontamination of MDA Reagents for Single Cell Whole Genome Amplification”. PLoS ONE 6.10 (2011): e26161.
PUB | DOI | WoS | PubMed | Europe PMC
 
[18]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991643
Hess, M., Sczyrba, Alexander, Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., Mackie, R. I., Pennacchio, L. A., Tringe, S. G., Visel, A., Woyke, T., Wang, Z., and Rubin, E. M. “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen”. Science 331.6016 (2011): 463-467.
PUB | DOI | WoS | PubMed | Europe PMC
 
[17]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991615
Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Desai, N., Eisen, J. A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, Alexander, Shade, A., and Stevens, R. “Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project”. Stand Genomic Sci 3.3 (2010): 243-248.
PUB | DOI | PubMed | Europe PMC
 
[16]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020
Lamprecht, Anna-Lena, Margaria, Tiziana, Steffen, Bernhard, Sczyrba, Alexander, Hartmeier, Sven, and Giegerich, Robert. “GeneFisher-P: variations of GeneFisher as processes in Bio-jETI”. BMC Bioinformatics 9.Suppl 4 (2008): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[15]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303
Sczyrba, Alexander, Konermann, Susanne, and Giegerich, Robert. “Two interactive bioinformatics courses at the bielefeld university bioinformatics server”. BRIEFINGS IN BIOINFORMATICS 9.3 (2008): 243-249.
PUB | DOI | WoS | PubMed | Europe PMC
 
[14]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
Spitzer, M, Lorkowski, S, Cullen, P, Sczyrba, Alexander, and Fuellen, Georg. “IsoSVM - Distinguishing isoforms and paralogs on the protein level”. BMC Bioinformatics 7.1 (2006): 110.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[13]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773613
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H., Giegerich, Robert, and Altmann, Curtis R. “XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis”. BMC Genomics 6.1 (2005): 123.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[12]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383529
Beckstette, Michael, Mailänder, Jens T., Marhöfer, Richard J., Sczyrba, Alexander, Ohlebusch, Enno, Giegerich, Robert, and Selzer, Paul M. “Genlight: Interactive high-throughput sequence analysis and comparative genomics”. Journal of Integrative Bioinformatics 1.1 (2004): 0008.
PUB | DOI
 
[11]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536
Beckstette, Michael, Sczyrba, Alexander, and Selzer, P.M. “Genlight: Interactive high-throughput sequence analysis and comparative genomics”. Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI, 2004. 179-186.
PUB
 
[10]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383561
Sczyrba, Alexander, Beckstette, Michael, Giegerich, Robert, and Altman, C. “Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis”. Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI, 2004.
PUB
 
[9]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, and Morgenstern, B. “AGenDA: gene prediction by cross-species sequence comparison”. Nucleic Acids Research 32.Web Server (2004): W305-W308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[8]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, and Giegerich, Robert. “e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences”. NUCLEIC ACIDS RESEARCH 32.Web Server (2004): W301-W304.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[7]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609260
Dondrup, M., Goesmann, Alexander, Bartels, D., Kalinowski, Jörn, Krause, L., Linke, Burkhard, Rupp, O., Sczyrba, Alexander, Pühler, Alfred, and Meyer, F. “EMMA: a platform for consistent storage and efficient analysis of microarray data”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 135-146.
PUB | DOI | WoS | PubMed | Europe PMC
 
[6]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612470
Morgenstern, B, Goel, S, Sczyrba, Alexander, and Dress, Andreas. “AltAVisT: Comparing alternative multiple sequence alignments”. BIOINFORMATICS 19.3 (2003): 425-426.
PUB | DOI | WoS | PubMed | Europe PMC
 
[5]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, and Giegerich, Robert. “RNA-related tools on the Bielefeld Bioinformatics Server”. Nucleic Acids Research 31.13 (2003): 3767-3770.
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
[4]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610494
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, Brudno, M, Batzoglou, S, and Morgenstern, B. “AGenDA: homology-based gene prediction”. BIOINFORMATICS 19.12 (2003): 1575-1577.
PUB | DOI | WoS | PubMed | Europe PMC
 
[3]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897716
Gopal, S., Schroeder, M., Pieper, U., Sczyrba, Alexander, Aytekin-Kurban, G., Bekiranov, S., Fajardo, J.E., Eswar, N., Sanchez, R., Sali, A., and Gaasterland, T. “Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome”. Nat Genet 27.3 (2001): 337-340.
PUB
 
[2]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1616752
Altmann, CR, Bell, E, Sczyrba, Alexander, Pun, J, Bekiranov, S, Gaasterland, T, and Brivanlou, AH. “Microarray-based analysis of early development in Xenopus laevis”. DEVELOPMENTAL BIOLOGY 236.1 (2001): 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[1]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897767
Gaasterland, T., Sczyrba, Alexander, Thomas, E., and Kurban, G. “MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region”. Genome Res 10.4 (2000): 502-510.
PUB
 

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[76]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2936223
Belmann, Peter, Fischer, Björn, Krüger, Jan, Procházka, Michal, Rasche, Helena, Prinz, Manuel, Hanussek, Maximilian, Lang, Martin, Bartusch, Felix, Gläßle, Benjamin, Krüger, Jens, Pühler, Alfred, and Sczyrba, Alexander. “de.NBI Cloud federation through ELIXIR AAI”. F1000Research 8 (2019): 842.
PUB | PDF | DOI | PubMed | Europe PMC
 
[75]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934798
Pankoke, Helga, Maus, Irena, Loh, Gunnar, Huser, Andrea, Seifert, Jana, Tilker, Alexandra, Hark, Sarah, Sczyrba, Alexander, Pelzer, Stefan, and Kleinbolting, Jessica. “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
 
[74]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2935923
Nelkner, Johanna, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “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): 424.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[73]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2933767
Fritz, Adrian, Hofmann, Peter, Majda, Stephan, Dahms, Eik, Dröge, Johannes, Fiedler, Jessika, Lesker, Till R., Belmann, Peter, DeMaere, Matthew Z., Darling, Aaron E., Sczyrba, Alexander, Bremges, Andreas, and McHardy, Alice C. “CAMISIM: simulating metagenomes and microbial communities”. Microbiome 7 (2019): 17.
PUB | DOI | WoS | PubMed | Europe PMC
 
[72]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2916929
Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants”. Microbial Biotechnology 11.4 (2018): 667-679.
PUB | DOI | WoS | PubMed | Europe PMC
 
[71]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920777
Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, and Wilke, Thomas. “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”. GigaScience 7.7 (2018): giy075.
PUB | DOI | WoS | PubMed | Europe PMC
 
[70]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920723
Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, and McHardy, Alice C. “AMBER: Assessment of Metagenome BinnERs”. GigaScience (2018): giy069.
PUB | DOI | WoS | PubMed | Europe PMC
 
[69]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930593
Linden, Mikael, Prochazka, Michal, Lappalainen, Ilkka, Bucik, Dominik, Vyskocil, Pavel, Kuba, Martin, Silén, Sami, Belmann, Peter, Sczyrba, Alexander, Newhouse, Steven, Matyska, Ludek, and Nyrönen, Tommi. “Common ELIXIR Service for Researcher Authentication and Authorisation”. F1000Research 7 (2018): 1199.
PUB | DOI | Download (ext.) | PubMed | Europe PMC
 
[68]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915890
Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. “Analyzing large scale genomic data on the cloud with Sparkhit”. Bioinformatics 34.9 (2018): 1457-1465.
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2920750
Maus, Irena, Rumming, Madis, Bergmann, Ingo, Heeg, Kathrin, Pohl, Marcel, Nettmann, Edith, Jaenicke, Sebastian, Blom, Jochen, Pühler, Alfred, Schlüter, Andreas, Sczyrba, Alexander, and Klocke, Michael. “Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors”. Biotechnology for Biofuels 11 (2018): 167.
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918275
Fleming, E. J., Woyke, T., Donatello, A. R., Kuypers, M. M. M., Sczyrba, Alexander, Littmann, S., and Emerson, D. “Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea”. Applied and Environmental Microbiology 84.9 (2018): e02239-17.
PUB | DOI | WoS | PubMed | Europe PMC
 
[65]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914959
da Schoren Costa, Pedro, Bolzan de Campos, Samanta, Albersmeier, Andreas, Dirksen, Paul, Pereira Dresseno, André Luis, Andrade Pais dos Santos, Odair José, Lima Milani, Karina Maria, Etto, Rafael Mazer, Battistus, André Gustavo, Peres Rodrigues da Costa, Andréia Cristina, Martinez de Oliveira, André Luiz, Weigert Galvão, Carolina, Guimarães, Vandeir Francisco, Sczyrba, Alexander, Wendisch, Volker F., and Passaglia, Luciane. “Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach”. Plant and Soil 422.1-2 (2018): 467-478.
PUB | DOI | WoS
 
[64]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909153
Yu, Jia, Blom, Jochen, Sczyrba, Alexander, and Goesmann, Alexander. “Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism”. Journal of Biotechnology 257 (2017): 58-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
[63]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, Albaum, Stefan, Schlüter, Andreas, Goesmann, Alexander, Sczyrba, Alexander, and Stoye, Jens. “Bioinformatics for NGS-based metagenomics and the application to biogas research”. Journal of Biotechnology 261.SI (2017): 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[62]
2017 | Datenpublikation | PUB-ID: 2914921
Huang, Liren, Krüger, Jan, and Sczyrba, Alexander. Sparkhit evaluation data set. Bielefeld University, 2017.
PUB | Dateien verfügbar | DOI
 
[61]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2915516
Maus, Irena, Bremges, Andreas, Stolze, Yvonne, Hahnke, Sarah, Cibis, Katharina G., Koeck, Daniela E., Kim, Yong S., Kreubel, Jana, Hassa, Julia, Wibberg, Daniel, Weimann, Aaron, Off, Sandra, Stantscheff, Robbin, Zverlov, Vladimir V., Schwarz, Wolfgang H., König, Helmut, Liebl, Wolfgang, Scherer, Paul, McHardy, Alice C., Sczyrba, Alexander, Klocke, Michael, Pühler, Alfred, and Schlüter, Andreas. “Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes”. Biotechnology for Biofuels 10.1 (2017): 264.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367
Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiūtė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton K H, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, and McHardy, Alice C. “Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software”. Nature Methods 14.11 (2017): 1063-1071.
PUB | DOI | WoS | PubMed | Europe PMC
 
[59]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904815
Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, and Schlüter, Andreas. “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): 156.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907633
Lux, Markus, Krüger, Jan, Rinke, Christian, Maus, Irena, Schlüter, Andreas, Woyke, Tanja, Sczyrba, Alexander, and Hammer, Barbara. “acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data”. BMC Bioinformatics 17 (2016): 543.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904836
Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E., Schlüter, Andreas, Sczyrba, Alexander, and Reichl, U. “Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type”. Biotechnology for Biofuels 9.1 (2016): 155.
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903489
Maus, Irena, Cibis, Katharina Gabriela, Bremges, Andreas, Stolze, Yvonne, Wibberg, Daniel, Tomazetto, Geizecler, Blom, Jochen, Sczyrba, Alexander, König, Helmut, Pühler, Alfred, and Schlüter, Andreas. “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): 50-60.
PUB | DOI | WoS | PubMed | Europe PMC
 
[55]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903302
Wibberg, Daniel, Bremges, Andreas, Dammann-Kalinowski, Tanja, Maus, Irena, Igeño, Maria Isabel, Vogelsang, Ralph, König, Christoph, Luque-Almagro, Víctor M., Roldán, Maria Dolores, Sczyrba, Alexander, Moreno-Vivián, Conrado, Blasco, Rafael, Pühler, Alfred, and Schlüter, Andreas. “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): 61-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
[54]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901418
Campos, Samanta B., Lisboa, Bruno B., Camargo, Flavio A.O., Bayer, Cimelio, Sczyrba, Alexander, Dirksen, Paul, Albersmeier, Andreas, Kalinowski, Jörn, Beneduzi, Anelise, Costa, Pedro B., Passaglia, Luciane Maria P., Vargas, Luciano K., and Wendisch, Volker F. “Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems”. Soil Biology and Biochemistry 96 (2016): 191-197.
PUB | DOI | WoS
 
[53]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2902190
Stiefel, Fabian, Fischer, Simon, Sczyrba, Alexander, Otte, Kerstin, and Hesse, Friedemann. “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): 31-43.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901729
Bremges, Andreas, Singer, Esther, Woyke, Tanja, and Sczyrba, Alexander. “MeCorS: Metagenome-enabled error correction of single cell sequencing reads”. Bioinformatics 32.14 (2016): 2199-2201.
PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901675
Krahn, Thomas, Wibberg, Daniel, Maus, Irena, Winkler, Anika, Bontron, Séverine, Sczyrba, Alexander, Nordmann, Patrice, Pühler, Alfred, Poirel, Laurent, and Schlüter, Andreas. “Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii blaNDM-1 carbapenemase gene.”. Antimicrobial Agents and Chemotherapy 60.5 (2016): 3032-3040.
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900928
Nesme, Joseph, Achouak, Wafa, Agathos, Spiros, Bailey, Mark, Baldrian, Petr, Brunel, Dominique, Frostegard, Asa, Heulin, Thierry, Jansson, Janet K., Jurkevitch, Edouard, Kowalchuk, George A., Kruus, Kristiina Leena, Lagares, Antonio, Lapin-Scott, Hilary M., Le Paslier, Denis, ic-Mulec, Ines, Murrell, Colin, Myrold, David D., Nalin, Renaud, Nannipieri, Paolo, Neufeld, Josh David, O'Gara, Fergal, Parnell, John Jacob, Pühler, Alfred, Pylro, Victor, Ramos, Juan Luis, Roesch, Luiz, Schleper, Christa, Schloter, Michael, Sczyrba, Alexander, Sessitsch, Angela, Sjöling, Sara, Sørensen, Jan, Sørensen, Søren J, Tebbe, Christoph C., Topp, Ed, Tsiamis, George, Van Elsas, Jan Dirk, Van Keulen, Geertje, Wagner, Michael, Widmer, Franco, Zhang, Tong, Zhang, Xiaojun, Zhao, Liping, Zhu, Yong-Guan, Vogel, Timothy M., and Simonet, Pascal. “Back to the future of soil metagenomics”. Frontiers in Microbiology 7 (2016): 73.
PUB | DOI | WoS | PubMed | Europe PMC
 
[49]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905260
Maus, Irena, Koeck, Daniela E., Cibis, Katharina G., Hahnke, Sarah, Kim, Yong S., Langer, Thomas, Kreubel, Jana, Erhard, Marcel, Bremges, Andreas, Off, Sandra, Stolze, Yvonne, Jaenicke, Sebastian, Goesmann, Alexander, Sczyrba, Alexander, Scherer, Paul, König, Helmut, Schwarz, Wolfgang H., Zverlov, Vladimir V., Liebl, Wolfgang, Pühler, Alfred, Schlüter, Andreas, and Klocke, Michael. “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): 171.
PUB | DOI | WoS | PubMed | Europe PMC
 
[48]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2904234
Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan, Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, and Schlüter, Andreas. “An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant”. Journal of Biotechnology 231 (2016): 268-279.
PUB | DOI | WoS | PubMed | Europe PMC
 
[47]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764906
Bremges, Andreas, Maus, Irena, Belmann, Peter, Eikmeyer, Felix Gregor, Winkler, Anika, Albersmeier, Andreas, Pühler, Alfred, Schlüter, Andreas, and Sczyrba, Alexander. “Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant”. GigaScience 4.1 (2015): 33.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2762833
Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, and Reichl, Udo. “Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities”. Proteomics 15.20 (2015): 3585-3589.
PUB | DOI | WoS | PubMed | Europe PMC
 
[45]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726183
Field, Erin K., Sczyrba, Alexander, Lyman, Audrey E., Harris, Christopher C., Woyke, Tanja, Stepanauskas, Ramunas, and Emerson, David. “Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount”. The ISME journal 9 (2015): 857-870.
PUB | DOI | WoS | PubMed | Europe PMC
 
[44]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2782501
Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C, Sczyrba, Alexander, and Barton, Michael D. “Bioboxes: standardised containers for interchangeable bioinformatics software”. GigaScience 4 (2015): 47.
PUB | DOI | WoS | PubMed | Europe PMC
 
[43]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901612
Lux, Markus, Sczyrba, Alexander, and Hammer, Barbara. “Automatic discovery of metagenomic structure”. 2015 International Joint Conference on Neural Networks (IJCNN). Institute of Electrical & Electronics Engineers (IEEE), 2015.
PUB | DOI
 
[42]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726156
Paul, Blair G., Bagby, Sarah C., Czornyj, Elizabeth, Arambula, Diego, Handa, Sumit, Sczyrba, Alexander, Ghosh, Partho, Miller, Jeff F., and Valentine, David L. “Targeted diversity generation by intraterrestrial archaea and archaeal viruses”. Nature Communications 6 (2015): 6585.
PUB | DOI | WoS | PubMed | Europe PMC
 
[41]
2015 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2901466
Osterholz, Benedikt, Wiebke, Pätzold, Fust, Annika, Rumming, Madis, Schlüter, Andreas, and Sczyrba, Alexander. “A Bioinformatics Pipeline for the Detection of β-lactamase Genes in Metagenome Sequence Data and its Application to Production-Scale Biogas Plants”. Presented at the 3rd International Symposium on the environmental Dimension of Antibiotic Resistance, Wernigerode, 2015.
PUB
 
[40]
2015 | Report | Veröffentlicht | PUB-ID: 2901613
Lux, Markus, Hammer, Barbara, and Sczyrba, Alexander. Automated Contamination Detection in Single-Cell Sequencing. Cold Spring Harbor Laboratory Press, 2015.
PUB | DOI
 
[39]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685992
Piao, Hailan, Lachman, Medora, Malfatti, Stephanie, Sczyrba, Alexander, Knierim, Bernhard, Auer, Manfred, Tringe, Susannah Green, Mackie, Roderick Ian, Yeoman, Carl James, and Hess, Matthias. “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).
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[38]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2654433
Kamke, Janine, Rinke, Christian, Schwientek, Patrick, Mavromatis, Kostas, Ivanova, Natalia, Sczyrba, Alexander, Woyke, Tanja, and Hentschel, Ute. “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): e87353.
PUB | DOI | WoS | PubMed | Europe PMC
 
[37]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689051
Ghylin, Trevor W., Garcia, Sarahi L., Moya, Francisco, Oyserman, Ben O., Schwientek, Patrick, Forest, Katrina T., Mutschler, James, Dwulit-Smith, Jeffrey, Chan, Leong-Keat, Martinez-Garcia, Manuel, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, Warnecke, Falk, Malmstrom, Rex, Bertilsson, Stefan, and McMahon, Katherine D. “Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage”. The ISME Journal 8.12 (2014): 2503-2516.
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2698163
Heins, Richard A, Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P, Chivian, Dylan C, Datta, Supratim, Friedland, Gregory D, D'Haeseleer, Patrik, Wu, Dongying, Tran-Gyamfi, Mary, Scullin, Chessa S, Singh, Seema, Shi, Weibing, Hamilton, Matthew G, Bendall, Matthew L, Sczyrba, Alexander, Thompson, John, Feldman, Taya, Guenther, Joel M, Gladden, John M, Cheng, Jan-Fang, Adams, Paul D, Rubin, Edward M, Simmons, Blake A, Sale, Kenneth L, Northen, Trent R, and Deutsch, Samuel. “Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry”. ACS chemical biology 9.9 (2014): 2082-2091.
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2672695
Swan, Brandon K., Chaffin, Mark D., Martinez-Garcia, Manuel, Morrison, Hilary G., Field, Erin K., Poulton, Nicole J., Masland, E. Dashiell P., Harris, Christopher C., Sczyrba, Alexander, Chain, Patrick S. G., Koren, Sergey, Woyke, Tanja, and Stepanauskas, Ramunas. “Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres”. PloS one 9.4 (2014): 95380.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
Henrich, Birgit, Rumming, Madis, Sczyrba, Alexander, Velleuer, Eunike, Dietrich, Ralf, Gerlach, Wolfgang, Gombert, Michael, Rahn, Sebastian, Stoye, Jens, Borkhardt, Arndt, and Fischer, Ute. “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”. PLoS ONE 9.3 (2014): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[33]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2662055
Wibberg, Daniel, Luque-Almagro, Víctor M., Igeño, M. Isabel, Bremges, Andreas, Roldán, M. Dolores, Merchán, Faustino, Sáez, Lara P., Guijo, M. Isabel, Manso, M. Isabel, Macías, Daniel, Cabello, Purificación, Becerra, Gracia, Ibáñez, M. Isabel, Carmona, M. Isabel, Escribano, M. Paz, Castillo, Francisco, Sczyrba, Alexander, Moreno-Vivián, Conrado, Blasco, Rafael, Pühler, Alfred, and Schlüter, Andreas. “Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344”. Journal of biotechnology 175 (2014): 67-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
[32]
2013 | Konferenzbeitrag | PUB-ID: 2909357
Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. IV. 2013. 174-179.
PUB
 
[31]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2623500
Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, and Sczyrba, Alexander. “Nonlinear dimensionality reduction for cluster identification in metagenomic samples”. 17th International Conference on Information Visualisation IV 2013. Ed. Ebad Banissi. 2013. 174-179.
PUB
 
[30]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613567
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N, Anderson, Iain J, Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K, Gies, Esther A, Dodsworth, Jeremy A, Hedlund, Brian P, Tsiamis, George, Sievert, Stefan M, Liu, Wen-Tso, Eisen, Jonathan A, Hallam, Steven J, Kyrpides, Nikos C, Stepanauskas, Ramunas, Rubin, Edward M, Hugenholtz, Philip, and Woyke, Tanja. “Insights into the phylogeny and coding potential of microbial dark matter”. Nature 499.7459 (2013): 431-437.
PUB | DOI | WoS | PubMed | Europe PMC
 
[29]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563424
Campbell, James H., O'Donoghue, Patrick, Campbell, Alisha G., Schwientek, Patrick, Sczyrba, Alexander, Woyke, Tanja, Söll, Dieter, and Podar, Mircea. “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): 5540-5545.
PUB | DOI | WoS | PubMed | Europe PMC
 
[28]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2638234
Zaremba-Niedzwiedzka, Katarzyna, Viklund, Johan, Zhao, Weizhou, Ast, Jennifer, Sczyrba, Alexander, Woyke, Tanja, McMahon, Katherina, Bertilsson, Stefan, Stepanauskas, Ramunas, and Andersson, Siv Ge. “Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade”. Genome biology 14.11 (2013): R130.
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641352
Kamke, Janine, Sczyrba, Alexander, Ivanova, Natalia, Schwientek, Patrick, Rinke, Christian, Mavromatis, Kostas, Woyke, Tanja, and Hentschel, Ute. “Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges”. The ISME journal 7.12 (2013): 2287-2300.
PUB | DOI | WoS | PubMed | Europe PMC
 
[26]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2563543
Campbell, Alisha G., Campbell, James H., Schwientek, Patrick, Woyke, Tanja, Sczyrba, Alexander, Allman, Steve, Beall, Clifford J., Griffen, Ann, Leys, Eugene, and Podar, Mircea. “Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity”. PLoS ONE 8.3 (2013): e59361.
PUB | DOI | WoS | PubMed | Europe PMC
 
[25]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2613623
Swan, Brandon K., Tupper, Ben, Sczyrba, Alexander, Lauro, Federico M., Martinez-Garcia, Manuel, González, José M., Luo, Haiwei, Wright, Jody J., Landry, Zachary C., Hanson, Niels W., Thompson, Brian P., Poulton, Nicole J., Schwientek, Patrick, Acinas, Silvia G., Giovannoni, Stephen J., Moran, Mary Ann, Hallam, Steven J., Cavicchioli, Ricardo, Woyke, Tanja, and Stepanauskas, Ramunas. “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): 11463-11468.
PUB | DOI | WoS | PubMed | Europe PMC
 
[24]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2518330
Garcia, Sarahi L, McMahon, Katherine D, Martinez-Garcia, Manuel, Srivastava, Abhishek, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, and Warnecke, Falk. “Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton”. The ISME journal 7.1 (2012): 137-147.
PUB | DOI | WoS | PubMed | Europe PMC
 
[23]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307
El-Kalioby, Mohamed, Abouelhoda, Mohamed, Krüger, Jan, Giegerich, Robert, Sczyrba, Alexander, Wall, Dennis P, and Tonellato, Peter. “Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package”. BMC Bioinformatics 13.Suppl 17 (2012): S22.
PUB | DOI | WoS | PubMed | Europe PMC
 
[22]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2329885
Swan, Brandon K., Martinez-Garcia, Manuel, Preston, Christina M., Sczyrba, Alexander, Woyke, Tanja, Lamy, Dominique, Reinthaler, Thomas, Poulton, Nicole J., Masland, E. Dashiell P., Gomez, Monica Lluesma, Sieracki, Michael E., DeLong, Edward F., Herndl, Gerhard J., and Stepanauskas, Ramunas. “Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean”. Science 333.6047 (2011): 1296-1300.
PUB | DOI | WoS | PubMed | Europe PMC
 
[21]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2351462
Kim, Tae-Wan, Chokhawala, Harshal A., Hess, Matthias, Dana, Craig M., Baer, Zachary, Sczyrba, Alexander, Rubin, Edward M., Blanch, Harvey W., and Clark, Douglas S. “High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery”. Angewandte Chemie 123.47 (2011): 11411-11414.
PUB | DOI | PubMed | Europe PMC
 
[20]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2789582
Sales, Christopher M., Mahendra, Shaily, Grostern, Ariel, Parales, Rebecca E, Goodwin, Lynne A, Woyke, Tanja, Nolan, Matt, Lapidus, Alla, Chertkov, Olga, Ovchinnikova, Galina, Sczyrba, Alexander, and Alvarez-Cohen, Lisa. “Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190”. Journal of Bacteriology 193.17 (2011): 4549-4550.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC | GenBank
 
[19]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410148
Woyke, Tanja, Sczyrba, Alexander, Lee, Janey, Rinke, Christian, Tighe, Damon, Clingenpeel, Scott, Malmstrom, Rex, Stepanauskas, Ramunas, and Cheng, Jan-Fang. “Decontamination of MDA Reagents for Single Cell Whole Genome Amplification”. PLoS ONE 6.10 (2011): e26161.
PUB | DOI | WoS | PubMed | Europe PMC
 
[18]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991643
Hess, M., Sczyrba, Alexander, Egan, R., Kim, T. W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., Mackie, R. I., Pennacchio, L. A., Tringe, S. G., Visel, A., Woyke, T., Wang, Z., and Rubin, E. M. “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen”. Science 331.6016 (2011): 463-467.
PUB | DOI | WoS | PubMed | Europe PMC
 
[17]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1991615
Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Desai, N., Eisen, J. A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, Alexander, Shade, A., and Stevens, R. “Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project”. Stand Genomic Sci 3.3 (2010): 243-248.
PUB | DOI | PubMed | Europe PMC
 
[16]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020
Lamprecht, Anna-Lena, Margaria, Tiziana, Steffen, Bernhard, Sczyrba, Alexander, Hartmeier, Sven, and Giegerich, Robert. “GeneFisher-P: variations of GeneFisher as processes in Bio-jETI”. BMC Bioinformatics 9.Suppl 4 (2008): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[15]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303
Sczyrba, Alexander, Konermann, Susanne, and Giegerich, Robert. “Two interactive bioinformatics courses at the bielefeld university bioinformatics server”. BRIEFINGS IN BIOINFORMATICS 9.3 (2008): 243-249.
PUB | DOI | WoS | PubMed | Europe PMC
 
[14]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
Spitzer, M, Lorkowski, S, Cullen, P, Sczyrba, Alexander, and Fuellen, Georg. “IsoSVM - Distinguishing isoforms and paralogs on the protein level”. BMC Bioinformatics 7.1 (2006): 110.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[13]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773613
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H., Giegerich, Robert, and Altmann, Curtis R. “XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis”. BMC Genomics 6.1 (2005): 123.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[12]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383529
Beckstette, Michael, Mailänder, Jens T., Marhöfer, Richard J., Sczyrba, Alexander, Ohlebusch, Enno, Giegerich, Robert, and Selzer, Paul M. “Genlight: Interactive high-throughput sequence analysis and comparative genomics”. Journal of Integrative Bioinformatics 1.1 (2004): 0008.
PUB | DOI
 
[11]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383536
Beckstette, Michael, Sczyrba, Alexander, and Selzer, P.M. “Genlight: Interactive high-throughput sequence analysis and comparative genomics”. Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI, 2004. 179-186.
PUB
 
[10]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383561
Sczyrba, Alexander, Beckstette, Michael, Giegerich, Robert, and Altman, C. “Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis”. Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI, 2004.
PUB
 
[9]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607400
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, and Morgenstern, B. “AGenDA: gene prediction by cross-species sequence comparison”. Nucleic Acids Research 32.Web Server (2004): W305-W308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[8]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1607394
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, and Giegerich, Robert. “e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences”. NUCLEIC ACIDS RESEARCH 32.Web Server (2004): W301-W304.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[7]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609260
Dondrup, M., Goesmann, Alexander, Bartels, D., Kalinowski, Jörn, Krause, L., Linke, Burkhard, Rupp, O., Sczyrba, Alexander, Pühler, Alfred, and Meyer, F. “EMMA: a platform for consistent storage and efficient analysis of microarray data”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 135-146.
PUB | DOI | WoS | PubMed | Europe PMC
 
[6]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612470
Morgenstern, B, Goel, S, Sczyrba, Alexander, and Dress, Andreas. “AltAVisT: Comparing alternative multiple sequence alignments”. BIOINFORMATICS 19.3 (2003): 425-426.
PUB | DOI | WoS | PubMed | Europe PMC
 
[5]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773844
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, and Giegerich, Robert. “RNA-related tools on the Bielefeld Bioinformatics Server”. Nucleic Acids Research 31.13 (2003): 3767-3770.
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
[4]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610494
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, Brudno, M, Batzoglou, S, and Morgenstern, B. “AGenDA: homology-based gene prediction”. BIOINFORMATICS 19.12 (2003): 1575-1577.
PUB | DOI | WoS | PubMed | Europe PMC
 
[3]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897716
Gopal, S., Schroeder, M., Pieper, U., Sczyrba, Alexander, Aytekin-Kurban, G., Bekiranov, S., Fajardo, J.E., Eswar, N., Sanchez, R., Sali, A., and Gaasterland, T. “Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome”. Nat Genet 27.3 (2001): 337-340.
PUB
 
[2]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1616752
Altmann, CR, Bell, E, Sczyrba, Alexander, Pun, J, Bekiranov, S, Gaasterland, T, and Brivanlou, AH. “Microarray-based analysis of early development in Xenopus laevis”. DEVELOPMENTAL BIOLOGY 236.1 (2001): 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[1]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897767
Gaasterland, T., Sczyrba, Alexander, Thomas, E., and Kurban, G. “MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region”. Genome Res 10.4 (2000): 502-510.
PUB
 

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