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1

CAMISIM: simulating metagenomes and microbial communities

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, Andr

Journal:

Year:

2019

Language:

english

File:

PDF, 6.09 MB

english, 2019

2

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

Bremges, Andreas, Maus, Irena, Belmann, Peter, Eikmeyer, Felix, Winkler, Anika, Albersmeier, Andreas, Pühler, Alfred, Schlüter, Andreas, Sczyrba, Alexander

Journal:

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

3

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

Heyer, R., Benndorf, D., Kohrs, F., De Vrieze, J., Boon, N., Hoffmann, M., Rapp, E., Schlüter, Andreas, Sczyrba, Alexander, Reichl, U.

Journal:

Biotechnology for Biofuels

Year:

2016

Language:

english

File:

PDF, 3.37 MB

english, 2016

4

Soil suppressiveness and its relations with the microbial community in a Brazilian subtropical agroecosystem under different management systems

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, Lu

Journal:

Soil Biology and Biochemistry

Year:

2016

Language:

english

File:

PDF, 756 KB

english, 2016

5

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka, Katarzyna, Viklund, Johan, Zhao, Weizhou, Ast, Jennifer, Sczyrba, Alexander, Woyke, Tanja, McMahon, Katherina, Bertilsson, Stefan, Stepanauskas, Ramunas, Andersson, Siv G E

Journal:

Year:

2013

Language:

english

File:

PDF, 708 KB

english, 2013

6

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism

Yu, Jia, Blom, Jochen, Sczyrba, Alexander, Goesmann, Alexander

Journal:

Journal of Biotechnology

Year:

2017

Language:

english

File:

PDF, 146 KB

english, 2017

7

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

Garcia, Sarahi L, McMahon, Katherine D, Martinez-Garcia, Manuel, Srivastava, Abhishek, Sczyrba, Alexander, Stepanauskas, Ramunas, Grossart, Hans-Peter, Woyke, Tanja, Warnecke, Falk

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 592 KB

english, 2013

8

Analyzing large scale genomic data on the cloud with Sparkhit

Huang, Liren, Krüger, Jan, Sczyrba, Alexander

Journal:

Year:

2017

Language:

english

File:

PDF, 1.55 MB

english, 2017

9

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

Lesker, Till R., Durairaj, Abilash C., GÃ¡lvez, Eric J.C., Lagkouvardos, Ilias, Baines, John F., Clavel, Thomas, Sczyrba, Alexander, McHardy, Alice C., Strowig, Till

Journal:

Year:

2020

File:

PDF, 46.07 MB

2020

10

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

Maus, Irena, Rumming, Madis, Bergmann, Ingo, Heeg, Kathrin, Pohl, Marcel, Nettmann, Edith, Jaenicke, Sebastian, Blom, Jochen, Pühler, Alfred, Schlüter, Andreas, Sczyrba, Alexander, Klocke, Michael

Journal:

Biotechnology for Biofuels

Year:

2018

Language:

english

File:

PDF, 1.92 MB

english, 2018

11

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

Kamke, Janine, Sczyrba, Alexander, Ivanova, Natalia, Schwientek, Patrick, Rinke, Christian, Mavromatis, Kostas, Woyke, Tanja, Hentschel, Ute

Journal:

The ISME Journal

Year:

2013

Language:

english

File:

PDF, 3.01 MB

english, 2013

12

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

Piao, Hailan, Lachman, Medora, Malfatti, Stephanie, Sczyrba, Alexander, Knierim, Bernhard, Auer, Manfred, Tringe, Susannah G., Mackie, Roderick I., Yeoman, Carl J., Hess, Matthias

Journal:

Frontiers in Microbiology

Year:

2014

Language:

english

File:

PDF, 7.86 MB

english, 2014

13

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

Stolze, Yvonne, Bremges, Andreas, Rumming, Madis, Henke, Christian, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, Schlüter, Andreas

Journal:

Biotechnology for Biofuels

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

14

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, Fischer, Simon, Sczyrba, Alexander, Otte, Kerstin, Hesse, Friedemann

Journal:

Journal of Biotechnology

Year:

2016

Language:

english

File:

PDF, 3.20 MB

english, 2016

15

GeneFisher-P: variations of GeneFisher as processes in Bio-jETI

Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier, Robert Giegerich

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.75 MB

english, 2008

16

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, Cibis, Katharina Gabriela, Bremges, Andreas, Stolze, Yvonne, Wibberg, Daniel, Tomazetto, Geizecler, Blom, Jochen, Sczyrba, Alexander, König, Helmut, Pühler, Alfred, Schlüter, Andreas

Journal:

Journal of Biotechnology

Year:

2016

Language:

english

File:

PDF, 765 KB

english, 2016

17

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

Lux, Markus, Krüger, Jan, Rinke, Christian, Maus, Irena, Schlüter, Andreas, Woyke, Tanja, Sczyrba, Alexander, Hammer, Barbara

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.29 MB

english, 2016

18

AMBER: Assessment of Metagenome BinnERs

Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, McHardy, Alice C

Journal:

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

19

[IEEE 2015 International Joint Conference on Neural Networks (IJCNN) - Killarney, Ireland (2015.7.12-2015.7.17)] 2015 International Joint Conference on Neural Networks (IJCNN) - Automatic discovery of metagenomic structure

Lux, Markus, Sczyrba, Alexander, Hammer, Barbara

Year:

2015

Language:

english

File:

PDF, 1011 KB

english, 2015

20

Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing

Wibberg, Daniel, Bremges, Andreas, Dammann-Kalinowski, Tanja, Maus, Irena, Igeño, Mª Isabel, Vogelsang, Ralph, König, Christoph, Luque-Almagro, Víctor M., Roldán, Mª Dolores, Sczyrba, Alexander, Moren

Journal:

Journal of Biotechnology

Year:

2016

Language:

english

File:

PDF, 1.52 MB

english, 2016

21

Binning enables efficient host genome reconstruction in cnidarian holobionts

Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, Wilke, Thomas

Journal:

Year:

2018

Language:

english

File:

PDF, 1.23 MB

english, 2018

22

XenDB: Full length cDNA prediction and cross species mapping inXenopus laevis

Alexander Sczyrba, Michael Beckstette, Ali H Brivanlou, Robert Giegerich, Curtis R Altmann

Journal:

Year:

2005

Language:

english

File:

PDF, 1.47 MB

english, 2005

23

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities

Kohrs, Fabian, Wolter, Sophie, Benndorf, Dirk, Heyer, Robert, Hoffmann, Marcus, Rapp, Erdmann, Bremges, Andreas, Sczyrba, Alexander, Schlüter, Andreas, Reichl, Udo

Journal:

Year:

2015

Language:

english

File:

PDF, 537 KB

english, 2015

24

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garr

Journal:

Year:

2017

Language:

english

File:

PDF, 5.62 MB

english, 2017

25

ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom

Moore, Marten, Wesemann, Corinna, Gossmann, Nikolaj, Sahm, Arne, KrÃ¼ger, Jan, Sczyrba, Alexander, Dietz, Karl-Josef

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.15 MB

2020

26

High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery

Dr. Tae-Wan Kim, Dr. Harshal A. Chokhawala, Dr. Matthias Hess, Craig M. Dana, Zachary Baer, Dr. Alexander Sczyrba, Prof. Edward M. Rubin, Prof. Harvey W. Blanch, Prof. Douglas S. Clark

Journal:

Angewandte Chemie

Year:

2011

Language:

english

File:

PDF, 591 KB

english, 2011

27

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Paul, Blair G., Bagby, Sarah C., Czornyj, Elizabeth, Arambula, Diego, Handa, Sumit, Sczyrba, Alexander, Ghosh, Partho, Miller, Jeff F., Valentine, David L.

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 933 KB

english, 2015

28

MeCorS: Metagenome-enabled error correction of single cell sequencing reads

Bremges, Andreas, Singer, Esther, Woyke, Tanja, Sczyrba, Alexander

Journal:

Year:

2016

Language:

english

File:

PDF, 143 KB

english, 2016

29

Insights into the phylogeny and coding potential of microbial dark matter

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, J

Journal:

Year:

2013

Language:

english

File:

PDF, 1.81 MB

english, 2013

30

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

Field, Erin K, Sczyrba, Alexander, Lyman, Audrey E, Harris, Christopher C, Woyke, Tanja, Stepanauskas, Ramunas, Emerson, David

Journal:

The ISME Journal

Year:

2014

Language:

english

File:

PDF, 2.57 MB

english, 2014

31

[IEEE 2013 17th International Conference on Information Visualisation - London, United Kingdom (2013.07.16-2013.07.18)] 2013 17th International Conference on Information Visualisation - Nonlinear Dimensionality Reduction for Cluster Identification in Metagenomic Samples

Gisbrecht, Andrej, Hammer, Barbara, Mokbel, Bassam, Sczyrba, Alexander

Year:

2013

Language:

english

File:

PDF, 761 KB

english, 2013

32

Intraspecies transfer of the chromosomally encoded Acinetobacter baumannii bla NDM-1 carbapenemase gene

Krahn, Thomas, Wibberg, Daniel, Maus, Irena, Winkler, Anika, Bontron, Séverine, Sczyrba, Alexander, Nordmann, Patrice, Pühler, Alfred, Poirel, Laurent, Schlüter, Andreas

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2016

Language:

english

File:

PDF, 1.12 MB

english, 2016

33

Genlight: Interactive high-throughput sequence analysis and comparative genomics

Beckstette, Michael, Mailänder, Jens T., Marhöfer, Richard J., Sczyrba, Alexander, Ohlebusch, Enno, Giegerich, Robert, Selzer, Paul M.

Journal:

Journal of Integrative Bioinformatics

Year:

2004

Language:

english

File:

PDF, 932 KB

english, 2004

34

Titelbild: High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery (Angew. Chem. 47/2011)

Dr. Tae-Wan Kim, Dr. Harshal A. Chokhawala, Dr. Matthias Hess, Craig M. Dana, Zachary Baer, Dr. Alexander Sczyrba, Prof. Edward M. Rubin, Prof. Harvey W. Blanch, Prof. Douglas S. Clark

Journal:

Angewandte Chemie

Year:

2011

File:

PDF, 949 KB

2011

35

10.1038/85922

Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, Eduardo Fajardo, J., Eswar, Narayanan, Sanchez, Roberto, Sali, Andrej, Gaasterland, Terry

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 52 KB

english, 2001

36

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, Henke, Christian, Lin, Timo Wentong, Pätzold, Wiebke, Hassa, Julia, Jaenicke, Sebastian, Grosch, Rita, Pühler, Alfred, Sczyrba, Alexander, Schlüter, Andreas

Journal:

Year:

2019

Language:

english

File:

PDF, 4.05 MB

english, 2019

37

Bioboxes: standardised containers for interchangeable bioinformatics software

Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C., Sczyrba, Alexander, Barton, Michael D.

Journal:

Year:

2015

Language:

english

File:

PDF, 720 KB

english, 2015

38

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

Stolze, Yvonne, Bremges, Andreas, Maus, Irena, Pühler, Alfred, Sczyrba, Alexander, Schlüter, Andreas

Journal:

Microbial Biotechnology

Year:

2017

Language:

english

File:

PDF, 325 KB

english, 2017

39

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

Ortseifen, Vera, Stolze, Yvonne, Maus, Irena, Sczyrba, Alexander, Bremges, Andreas, Albaum, Stefan P., Jaenicke, Sebastian, Fracowiak, Jochen, Pühler, Alfred, Schlüter, Andreas

Journal:

Journal of Biotechnology

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

40

F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota

Pankoke, Helga, Maus, Irena, Loh, Gunnar, Hüser, Andrea, Seifert, Jana, Tilker, Alexandra, Hark, Sarah, Sczyrba, Alexander, Pelzer, Stefan, Kleinbölting, Jessica

Journal:

FEMS Microbiology Letters

Year:

2019

Language:

english

File:

PDF, 1.19 MB

english, 2019

41

Cover Picture: High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery (Angew. Chem. Int. Ed. 47/2011)

Dr. Tae-Wan Kim, Dr. Harshal A. Chokhawala, Dr. Matthias Hess, Craig M. Dana, Zachary Baer, Dr. Alexander Sczyrba, Prof. Edward M. Rubin, Prof. Harvey W. Blanch, Prof. Douglas S. Clark

Journal:

Angewandte Chemie International Edition

Year:

2011

Language:

english

File:

PDF, 1.22 MB

english, 2011

42

EMMA: a platform for consistent storage and efficient analysis of microarray data

Michael Dondrup, Alexander Goesmann, Daniela Bartels, Jörn Kalinowski, Lutz Krause, Burkhard Linke, Oliver Rupp, Alexander Sczyrba, Alfred Pühler, Folker Meyer

Journal:

Journal of Biotechnology

Year:

2003

Language:

english

File:

PDF, 687 KB

english, 2003

43

Bioinformatics for NGS-based Metagenomics and the Application to Biogas Research

Jünemann, Sebastian, Kleinbölting, Nils, Jaenicke, Sebastian, Henke, Christian, Hassa, Julia, Nelkner, Johanna, Stolze, Yvonne, Albaum, Stefan P., Schlüter, Andreas, Goesmann, Alexander, Sczyrba, Alex

Journal:

Journal of Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.02 MB

english, 2017

44

High-Throughput In Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery

Dr. Tae-Wan Kim, Dr. Harshal A. Chokhawala, Dr. Matthias Hess, Craig M. Dana, Zachary Baer, Dr. Alexander Sczyrba, Prof. Edward M. Rubin, Prof. Harvey W. Blanch, Prof. Douglas S. Clark

Journal:

Angewandte Chemie International Edition

Year:

2011

Language:

english

File:

PDF, 573 KB

english, 2011

45

IsoSVM – Distinguishing isoforms and paralogs on the protein level

Michael Spitzer, Stefan Lorkowski, Paul Cullen, Alexander Sczyrba, Georg Fuellen

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 964 KB

english, 2006

46

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum

Rettenmaier, Regina, Schneider, Martina, Munk, Bernhard, Lebuhn, Michael, JÃ¼nemann, Sebastian, Sczyrba, Alexander, Maus, Irena, Zverlov, Vladimir, Liebl, Wolfgang

Journal:

Year:

2020

File:

PDF, 1.58 MB

2020

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