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A community proposal to integrate proteomics activities in ELIXIR. Vizcaíno JA et al. F1000Res. (2017)

Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T. Torres Tejerizo G et al. Genome Announc. (2017)

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Maus I et al. Biotechnol Biofuels. (2017)

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Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics.

Nelkner J, Tejerizo GT, Hassa J, Lin TW, Witte J, Verwaaijen B, Winkler A, Bunk B, Spröer C, Overmann J, Grosch R, Pühler A, Schlüter AA.

Genes (Basel). 2019 Aug 9;10(8). pii: E601. doi: 10.3390/genes10080601.


de.NBI Cloud federation through ELIXIR AAI.

Belmann P, Fischer B, Krüger J, Procházka M, Rasche H, Prinz M, Hanussek M, Lang M, Bartusch F, Gläßle B, Krüger J, Pühler A, Sczyrba A.

F1000Res. 2019 Jun 10;8:842. doi: 10.12688/f1000research.19013.1. eCollection 2019.


Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110.

Schaffert L, März C, Burkhardt L, Droste J, Brandt D, Busche T, Rosen W, Schneiker-Bekel S, Persicke M, Pühler A, Kalinowski J.

Microb Cell Fact. 2019 Jun 28;18(1):114. doi: 10.1186/s12934-019-1162-5.


Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes.

Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A.

Genes (Basel). 2019 Jun 3;10(6). pii: E424. doi: 10.3390/genes10060424.


A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani.

Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A.

Sci Rep. 2019 May 10;9(1):7221. doi: 10.1038/s41598-019-43706-5.


Insight into the structure, function and conjugative transfer of pLPU83a, an accessory plasmid of Rhizobium favelukesii LPU83.

Castellani LG, Nilsson JF, Wibberg D, Schlüter A, Pühler A, Brom S, Pistorio M, Torres Tejerizo G.

Plasmid. 2019 May;103:9-16. doi: 10.1016/j.plasmid.2019.03.004. Epub 2019 Mar 27.


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

Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M.

Biotechnol Biofuels. 2018 Jun 19;11:167. doi: 10.1186/s13068-018-1162-4. eCollection 2018.


Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A.

Biotechnol Rep (Amst). 2018 Apr 30;18:e00254. doi: 10.1016/j.btre.2018.e00254. eCollection 2018 Jun.


Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase.

Alkhateeb RS, Vorhölter FJ, Steffens T, Rückert C, Ortseifen V, Hublik G, Niehaus K, Pühler A.

Appl Microbiol Biotechnol. 2018 Aug;102(15):6613-6625. doi: 10.1007/s00253-018-9106-2. Epub 2018 Jun 1.


Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats.

Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M.

Sci Rep. 2018 May 17;8(1):7783. doi: 10.1038/s41598-018-26180-3.


Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.

Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A.

Appl Microbiol Biotechnol. 2018 Jun;102(12):5045-5063. doi: 10.1007/s00253-018-8976-7. Epub 2018 Apr 30. Review.


Complete Genome Sequencing of Acinetobacter baumannii Strain K50 Discloses the Large Conjugative Plasmid pK50a Encoding Carbapenemase OXA-23 and Extended-Spectrum β-Lactamase GES-11.

Wibberg D, Salto IP, Eikmeyer FG, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A.

Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e00212-18. doi: 10.1128/AAC.00212-18. Print 2018 May.


Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A.

J Biotechnol. 2018 Feb 10;267:12-18. doi: 10.1016/j.jbiotec.2017.12.021. Epub 2017 Dec 24.


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

Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A.

Microb Biotechnol. 2018 Jul;11(4):667-679. doi: 10.1111/1751-7915.12982. Epub 2017 Dec 4.


Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.

Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A.

Biotechnol Biofuels. 2017 Nov 13;10:264. doi: 10.1186/s13068-017-0947-1. eCollection 2017.


A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M.

Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]


Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors.

Lasek R, Dziewit L, Ciok A, Decewicz P, Romaniuk K, Jedrys Z, Wibberg D, Schlüter A, Pühler A, Bartosik D.

J Biotechnol. 2017 Dec 10;263:64-74. doi: 10.1016/j.jbiotec.2017.09.011. Epub 2017 Sep 15.


The complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) carrying gene clusters for the biosynthesis of tetracenomycin C, 5`-hydroxy streptomycin, and acarbose.

Ortseifen V, Kalinowski J, Pühler A, Rückert C.

J Biotechnol. 2017 Nov 20;262:84-88. doi: 10.1016/j.jbiotec.2017.09.008. Epub 2017 Sep 14.


Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685.

Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schlüter A, Pühler A, Bartosik D.

Environ Microbiol. 2017 Nov;19(11):4536-4550. doi: 10.1111/1462-2920.13901. Epub 2017 Oct 13.


The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.

Wolf T, Droste J, Gren T, Ortseifen V, Schneiker-Bekel S, Zemke T, Pühler A, Kalinowski J.

BMC Genomics. 2017 Jul 25;18(1):562. doi: 10.1186/s12864-017-3941-x.

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