3088 Publications

2018 | Journal Article | PUB-ID: 2921269
Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R (2018)
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.
mSystems 3(3): e00218-17.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2921264
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R, Mann AE, Amir A, Frazier A, Martino C, Lebrilla C, Lozupone C, Lewis CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Lovelace E, Pierce E, TerAvest E, Bolyen E, Bushman FD, Wu GD, Church GM, Saxe G, Holscher HD, Ugrina I, German JB, Caporaso JG, Wozniak JM, Kerr J, Ravel J, Lewis JD, Suchodolski JS, Jansson JK, Hampton-Marcell JT, Bobe J, Raes J, Chase JH, Eisen JA, Monk J, Clemente JC, Petrosino J, Goodrich J, Gauglitz J, Jacobs J, Zengler K, Swanson KS, Lewis K, Mayer K, Bittinger K, Dillon L, Zaramela LS, Schriml LM, Dominguez-Bello MG, Jankowska MM, Blaser M, Pirrung M, Minson M, Kurisu M, Ajami N, Gottel NR, Chia N, Fierer N, White O, Cani PD, Gajer P, Strandwitz P, Kashyap P, Dutton R, Park RS, Xavier RJ, Mills RH, Krajmalnik-Brown R, Ley R, Owens SM, Klemmer S, Matamoros S, Mirarab S, Moorman S, Holmes S, Schwartz T, Eshoo-Anton TW, Vigers T, Pandey V, Treuren WV, Fang X, Zech Xu Z, Jarmusch A, Geier J, Reeve N, Silva R, Kopylova E, Nguyen D, Sanders K, Salido Benitez RA, Heale AC, Abramson M, Waldispühl J, Butyaev A, Drogaris C, Nazarova E, Ball M, Gunderson B (2018)
American Gut: an Open Platform for Citizen Science Microbiome Research.
mSystems 3(3): e00031-18.
PUB | DOI
 
2018 | Book Chapter | PUB-ID: 2921257
Heux S, Brautaset T, Vorholt JA, Wendisch VF, Portais J-C (2018)
Synthetic Methylotrophy: Past, Present, and Future.
In: Methane Biocatalysis: Paving the Way to Sustainability. Kalyuzhnaya MG, Xing X-H (Eds); Cham: Springer: 133-152.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2921229
Schneider O, Ilic-Tomic T, Rückert C, Kalinowski J, Gencic MS, Zivkovic MZ, Stankovic N, Radulovic NS, Vasiljevic B, Nikodinovic-Runic J, Zotchev SB (2018)
Genomics-Based Insights Into the Biosynthesis and Unusually High Accumulation of Free Fatty Acids by Streptomyces sp NP10.
FRONTIERS IN MICROBIOLOGY 9: 10.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2921235
Wolf F, Leipoldt F, Kulik A, Wibberg D, Kalinowski J, Kaysser L (2018)
Characterization of the Actinonin Biosynthetic Gene Cluster.
CHEMBIOCHEM 19(11): 1189-1195.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919984
Neubauer P, Widmann C, Wibberg D, Schröder L, Frese M, Kottke T, Kalinowski J, Niemann H, Sewald N (2018)
A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination.
PLOS ONE 13(5): e0196797.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920750
Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M (2018)
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.
Biotechnology for Biofuels 11: 167.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2916929
Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A (2018)
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.
Microbial Biotechnology 11(4): 667-679.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2921210
Lauersen KJ, Wichmann J, Baier T, Kampranis SC, Pateraki I, Lindberg Møller B, Kruse O (In Press)
Phototrophic production of heterologous diterpenoids and a hydroxy-functionalized derivative from Chlamydomonas reinhardtii.
Metabolic Engineering.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2920989
Perez F, Wendisch VF (2018)
Transport and metabolic engineering of the cell factory Corynebacterium glutamicum.
FEMS Microbiology Letters.
PUB | DOI | PubMed | Europe PMC
 
2018 | Conference Paper | PUB-ID: 2921039
Langenkämper D, van Kevelaer R, Nattkemper TW (Accepted)
Strategies for Tackling the Class Imbalance Problem in Marine Image Classification.
Presented at the International Conference on Pattern Recognition 2018, Computer Vision for Automated Analysis of Underwater Imagery Workshop, Beijing.
PUB | PDF
 
2018 | Journal Article | PUB-ID: 2919149
Henke NA, Wichmann J, Baier T, Frohwitter J, Lauersen KJ, Risse JM, Peters-Wendisch P, Kruse O, Wendisch VF (2018)
Patchoulol production with metabolically engineered Corynebacterium glutamicum.
Genes 9(4): 219.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2921036
Harun I, del Río Chanona EA, Wagner JL, Lauersen KJ, Zhang D, Hellgardt K (Accepted)
Photocatalytic production of bisabolene from green microalgae mutant: process analysis and kinetic modelling.
Industrial & Engineering Chemistry Research.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2921026
Haak M, Vinke S, Keller W, Droste J, Rückert C, Kalinowski J, Pucker B (2018)
High Quality de Novo Transcriptome Assembly of Croton tiglium.
Frontiers in Molecular Biosciences 5: 62.
PUB | PDF | DOI
 
2018 | Journal Article | PUB-ID: 2920940
Kibret M, Guerrero-Garzon JF, Urban E, Zehl M, Wronski V-K, Rückert C, Busche T, Kalinowski J, Rollinger JM, Abate D, Zotchev SB (2018)
Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry.
FRONTIERS IN MICROBIOLOGY 9: 13.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919012
Jaenicke S, Albaum S, Blumenkamp P, Linke B, Stoye J, Goesmann A (2018)
Flexible metagenome analysis using the MGX framework.
Microbiome 6: 76.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920943
Blifernez-Klassen O, Chaudhari S, Klassen V, Wördenweber R, Steffens T, Cholewa D, Niehaus K, Kalinowski J, Kruse O (2018)
Metabolic survey of Botryococcus braunii: Impact of the physiological state on product formation.
PLOS ONE 13(6): 23.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920723
Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC (2018)
AMBER: Assessment of Metagenome BinnERs.
GigaScience: giy069.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2920777
Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T (2018)
Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts.
GigaScience: giy075.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2920779
Baier T, Wichmann J, Kruse O, Lauersen KJ (2018)
Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga Chlamydomonas reinhardtii.
Nucleic Acids Research: gky532.
PUB | DOI
 
2018 | Working Paper | PUB-ID: 2920633
Friedrich A, Pucker B (2018)
Peer-review as a teaching method. Working Paper der AG Forschendes Lernen in der dghd; 2, 2018.
Carl von Ossietzky Universität Oldenburg.
PUB | PDF
 
2018 | Journal Article | PUB-ID: 2920679
Busche T, Tsolis KC, Koepff J, Rebets Y, Rückert C, Hamed MB, Bleidt A, Wiechert W, Lopatniuk M, Yousra A, Anne J, Karamanou S, Oldiges M, Kalinowski J, Luzhetskyy A, Economou A (2018)
Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion.
FRONTIERS IN MICROBIOLOGY 9: 12.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920680
Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski J, Ziemert N (2018)
Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.
BMC GENOMICS 19: 15.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920690
Schwentner A, Feith A, Muench E, Busche T, Rückert C, Kalinowski J, Takors R, Blombach B (2018)
Metabolic engineering to guide evolution - Creating a novel mode for L-valine production with Corynebacterium glutamicum.
METABOLIC ENGINEERING 47: 31-41.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920691
Spohn M, Edenhart S, Alanjary M, Ziemert N, Wibberg D, Kalinowski J, Niedermeyer THJ, Stegmann E, Wohlleben W (2018)
Identification of a novel aminopolycarboxylic acid siderophore gene cluster encoding the biosynthesis of ethylenediaminesuccinic acid hydroxyarginine (EDHA).
METALLOMICS 10(5): 722-734.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920701
Ribicic D, Netzer R, Winkler A, Brakstad OG (2018)
Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures.
MARINE POLLUTION BULLETIN 129(1): 308-317.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920704
Frickmann H, Koeller T, Hagen RM, Ebert K-P, Mueller M, Wenzel W, Gatzer R, Schotte U, Binder A, Skusa R, Warnke P, Podbielski A, Rückert C, Kreikemeyer B (2018)
Molecular Epidemiology of Multidrug-Resistant Bacteria Isolated from Libyan and Syrian Patients with War Injuries in Two Bundeswehr Hospitals in Germany.
EUROPEAN JOURNAL OF MICROBIOLOGY AND IMMUNOLOGY 8(1): 1-11.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919005
Schulz T, Stoye J, Dörr D (2018)
GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data.
BMC Genomics 19(Suppl. 5): 308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919006
Rubert DP, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2018)
Computing the family-free DCJ similarity.
BMC Bioinformatics 19(Suppl. 6): 152.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918275
Fleming EJ, Woyke T, Donatello AR, Kuypers MMM, Sczyrba A, Littmann S, Emerson D (2018)
Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea.
Applied and Environmental Microbiology 84(9): e02239-17.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920259
Heine T, Zimmerling J, Ballmann A, Kleeberg SB, Rückert C, Busche T, Winkler A, Kalinowski J, Poetsch A, Scholtissek A, Oelschlaegel M, Schmidt G, Tischler D (2018)
On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY 84(9): 16.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920267
Zirpel B, Degenhardt F, Zammarelli C, Wibberg D, Kalinowski J, Stehle F, Kayser O (2018)
Optimization of Delta(9)-tetrahydrocannabinolic acid synthase production in Komagataella phaffii via post-translational bottleneck identification.
JOURNAL OF BIOTECHNOLOGY 272: 40-47.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920275
Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, Schlüter A, Schellenberg I (2018)
Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.
PLOS ONE 13(4): 32.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920311
Abdali N, Younas F, Mafakheri S, Pothula KR, Kleinekathoefer U, Tauch A, Benz R (2018)
Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109.
BMC BIOCHEMISTRY 19: 18.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920173
Wibberg D, Salto IP, Eikmeyer FG, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A (2018)
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.
Antimicrobial Agents and Chemotherapy 62(5): e00212-18.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920330
Robledo M, Schlueter J-P, Loehr LO, Linne U, Albaum S, Jimenez-Zurdo JI, Becker A (2018)
An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.
FRONTIERS IN MICROBIOLOGY 9: 14.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920334
Brakstad OG, Ribicic D, Winkler A, Netzer R (2018)
Biodegradation of dispersed oil in seawater is not inhibited by a commercial oil spill dispersant.
MARINE POLLUTION BULLETIN 129(2): 555-561.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919914
Wendisch VF, Kim Y, Lee J-H (2018)
Chemicals from lignin. Recent depolymerization techniques and upgrading extended pathways.
Current Opinion in Green and Sustainable Chemistry 14: 33-39.
PUB | DOI
 
2018 | Bielefeld Dissertation | PUB-ID: 2919935
Hattab G (2018)
Analyzing colony dynamics and visualizing cell diversity in spatiotemporal experiments.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2018 | Journal Article | PUB-ID: 2917037
Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A (2018)
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.
JOURNAL OF BIOTECHNOLOGY 267: 12-18.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920170
Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A (2018)
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.
Applied Microbiology and Biotechnology 102(12): 5045-5063.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920168
Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A (2018)
Proteiniphilum saccharofermentans str. M3/6 T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.
Biotechnology Reports 18: e00254.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2915890
Huang L, Krüger J, Sczyrba A (2018)
Analyzing large scale genomic data on the cloud with Sparkhit.
Bioinformatics 34(9): 1457-1465.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920169
Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M (2018)
Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats.
Scientific Reports 8(1): 7783.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918840
Sgobba E, Stumpf AK, Vortmann M, Jagmann N, Krehenbrink M, Dirks-Hofmeister ME, Moerschbacher B, Philipp B, Wendisch VF (2018)
Synthetic Escherichia coli-Corynebacterium glutamicum consortia for L-lysine production from starch and sucrose.
Biores Technol 260: 302-310.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920160
Arnold W, Grotjohann N, Pühler A, Röllke K, Selbitschka W (2018)
Die CeBiT ec Schülerakademie „Synthetische Biologie/Biotechnologie “– Begabtenförderung in einem zukunftsträchtigen Forschungsfeld.
ABB-Information. Jahresheft 2017.
PUB
 
2018 | Journal Article | PUB-ID: 2919346
Hagenfeld D, Koch R, Jünemann S, Prior K, Harks I, Eickholz P, Hoffmann T, Kim T-S, Kocher T, Meyle J, Kaner D, Schlagenhauf U, Ehmke B, Harmsen D (2018)
Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis.
PLOS ONE 13(4): e0195534.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2920133
Ruwe M, Rückert C, Kalinowski J, Persicke M (2018)
Functional characterization of a small Alarmone Hydrolase in Corynebacterium glutamicum.
Frontiers in Microbiology 9: 916.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2913367
Baumgart M, Unthan S, Kloss R, Radek A, Polen T, Tenhaef N, Müller MF, Küberl A, Siebert D, Brühl N, Marin K, Hans S, Krämer R, Bott M, Kalinowski J, Wiechert W, Seibold G, Frunzke J, Rückert C, Wendisch VF, Noack S (2018)
Corynebacterium glutamicum chassis C1*: Building and testing a novel platform host for synthetic biology and industrial biotechnology.
ACS Synthetic Biology 7: 132–144.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918481
Luhmann N, Chauve C, Stoye J, Wittler R (Accepted)
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
PUB | DOI
 

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