3051 Publications

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
 
2018 | Journal Article | PUB-ID: 2919914
Wendisch VF, Kim Y, Lee J-H (Accepted)
Chemicals from lignin: Recent depolymerization techniques and upgrading extended pathways.
Curr Op Green Sust Chem.
PUB
 
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: 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 | DOI
 
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 | DOI
 
2018 | Bielefeld Dissertation | PUB-ID: 2919356
Willing E (2018)
On Distance and Sorting of the Double Cut-and-Join and the Inversion-*indel* Model.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
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
 
2018 | Journal Article | PUB-ID: 2919299
Wagner C, Bonte A, Bruehl L, Niehaus K, Bednarz H, Matthaeus B (2018)
Micro-organisms growing on rapeseed during storage affect the profile of volatile compounds of virgin rapeseed oil.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 98(6): 2147-2155.
PUB | DOI | WoS | PubMed | Europe PMC
 
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
 
2018 | Journal Article | PUB-ID: 2918160
Wendisch VF, Mindt M, Perez F (2018)
Biotechnological production of mono- and diamines using bacteria: recent progress, applications and perspectives.
Appl Microbiol Biotechnol 102(8): 3583-3594.
PUB | DOI | WoS | PubMed | Europe PMC
 
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: 219.
PUB | DOI | PubMed | Europe PMC
 
2018 | Bielefeld Dissertation | PUB-ID: 2918485
Holley G (2018)
Pan-genome Search and Storage.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2018 | Journal Article | PUB-ID: 2918205
Pechtl A, Rückert C, Maus I, Koeck DE, Trushina N, Kornberger P, Schwarz WH, Schlüter A, Liebl W, Zverlov VV (2018)
Complete Genome Sequence of the Novel Cellulolytic, Anaerobic, Thermophilic Bacterium Herbivorax saccincola Type Strain GGR1, Isolated from a Lab Scale Biogas Reactor as Established by Illumina and Nanopore MinION Sequencing.
Genome Announcements 6(6): e01493-17.
PUB | DOI
 
2018 | Book (Editor) | PUB-ID: 2913920
Setubal JC, Stadler P, Stoye J (Eds) (2018)
Comparative Genomics: Methods and Protocols. Methods in Molecular Biology; 1704.
New York: Springer Verlag.
PUB
 
2018 | Book Chapter | PUB-ID: 2913922
Dörr D, Feijão P, Stoye J (2018)
Family-Free Genome Comparison.
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 331-342.
PUB
 
2018 | Book Chapter | PUB-ID: 2913921
Zekic T, Holley G, Stoye J (2018)
Pan-genome Storage and Analysis Techniques.
In: Comparative Genomics. Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. New York: Springer Verlag: 29-53.
PUB
 
2018 | Journal Article | PUB-ID: 2919053
Tsolis KC, Tsare E-P, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anne J, Karamanou S, Klapa MI, Economou A (2018)
Comprehensive subcellular topologies of polypeptides in Streptomyces.
MICROBIAL CELL FACTORIES 17: 12.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919058
Senges CHR, Al-Dilaimi A, Marchbank DH, Wibberg D, Winkler A, Haltli B, Nowrousian M, Kalinowski J, Kerr RG, Bandow JE (2018)
The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115(10): 2490-2495.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2919065
Cerletti M, Paggi R, Troetschel C, Celeste Ferrari M, Guevara CR, Albaum S, Poetsch A, De Castro R (2018)
LonB Protease Is a Novel Regulator of Carotenogenesis Controlling Degradation of Phytoene Synthase in Haloferax volcanii.
JOURNAL OF PROTEOME RESEARCH 17(3): 1158-1171.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918969
Busche T, Novakova R, Al'Dilaimi A, Homerova D, Feckova L, Rezuchova B, Mingyar E, Csolleiova D, Bekeova C, Winkler A, Sevcikova B, Kalinowski J, Kormanec J, Rückert C (2018)
Complete Genome Sequence of Streptomyces lavendulae subsp. lavendulae CCM 3239 (Formerly “Streptomyces aureofaciens CCM 3239”), a Producer of the Angucycline-Type Antibiotic Auricin.
Genome Announcements 6(9): e00103-18.
PUB | PDF | DOI
 
2018 | Journal Article | PUB-ID: 2917296
Wittchen M, Busche T, Gaspar AH, Lee JH, Ton-That H, Kalinowski J, Tauch A (2018)
Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation.
BMC Genomics 19(1): 82.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918668
Hamed A, Abdel-Razek AS, Frese M, Wibberg D, El-Haddad AF, Ibrahim TMA, Kalinowski J, Sewald N, Shaaban M (2018)
N-Acetylborrelidin B: a new bioactive metabolite from Streptomyces mutabilis sp MII.
ZEITSCHRIFT FÜR NATURFORSCHUNG SECTION C-A JOURNAL OF BIOSCIENCES 73(1-2): 49-57.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918662
Mori T, Cahn JKB, Wilson MC, Meoded RA, Wiebach V, Martinez AFC, Helfrich EJN, Albersmeier A, Wibberg D, Datwyler S, Keren R, Lavy A, Rückert C, Ilan M, Kalinowski J, Matsunaga S, Takeyama H, Piel J (2018)
Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115(8): 1718-1723.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918672
Koepff J, Morschett H, Busche T, Winkler A, Kalinowski J, Wiechert W, Oldiges M (2018)
Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans.
BIOTECHNOLOGY PROGRESS 34(1): 287-292.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2918674
Landwehr W, Kaempfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink J (2018)
Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp nov and Streptomyces davaonensis sp nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 68(1): 382-393.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2915928
Wichmann J, Baier T, Wentnagel E, Lauersen KJ, Kruse O (2018)
Tailored carbon partitioning for phototrophic production of (E)-α-bisabolene from the green microalga Chlamydomonas reinhardtii.
Metabolic Engineering 45: 211-222.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2914959
da Schoren Costa P, Bolzan de Campos S, Albersmeier A, Dirksen P, Pereira Dresseno AL, Andrade Pais dos Santos OJ, Lima Milani KM, Etto RM, Battistus AG, Peres Rodrigues da Costa AC, Martinez de Oliveira AL, Weigert Galvão C, Guimarães VF, Sczyrba A, Wendisch VF, Passaglia L (2018)
Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach.
Plant and Soil 422(1-2): 467-478.
PUB | DOI | WoS
 
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: AEM.02239-17.
PUB | DOI
 
2018 | Journal Article | PUB-ID: 2917735
Wagner M, Shen L, Albersmeier A, van der Kolk N, Kim S, Cha J, Brasen C, Kalinowski J, Siebers B, Albers S-V (2018)
Sulfolobus acidocaldarius Transports Pentoses via a Carbohydrate Uptake Transporter 2 (CUT2)-Type ABC Transporter and Metabolizes Them through the Aldolase-Independent Weimberg Pathway.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY 84(3): 19.
PUB | DOI | WoS
 
2018 | Journal Article | PUB-ID: 2917736
Vu VL, Busche T, Tedin K, Bernhardt J, Wollenhaupt J, Huyen NTT, Weise C, Kalinowski J, Wahl MC, Fulde M, Antelmann H (2018)
Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus.
ANTIOXIDANTS & REDOX SIGNALING: 22.
PUB | DOI | WoS | PubMed | Europe PMC
 
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: 2917042
Kranz A, Busche T, Vogel A, Usadel B, Kalinowski J, Bott M, Polen T (2018)
RNAseq analysis of alpha-proteobacterium Gluconobacter oxydans 621H.
BMC GENOMICS 19: 17.
PUB | DOI | WoS | PubMed | Europe PMC
 
2018 | Journal Article | PUB-ID: 2914092
Henke NA, Wiebke D, Perez F, Peters-Wendisch P, Wendisch VF (2018)
Coproduction of cell-bound and secreted value-added compounds: simultaneous production of carotenoids and amino acids by Corynebacterium glutamicum.
Bioresorce Technology 247: 744-752.
PUB | DOI | WoS
 
2017 | Journal Article | PUB-ID: 2913216
Venkanna D, Südfeld C, Baier T, Homburg SV, Patel A, Wobbe L, Kruse O (2017)
Knock-Down of the IFR1 Protein Perturbs the Homeostasis of Reactive Electrophile Species and Boosts Photosynthetic Hydrogen Production in Chlamydomonas reinhardtii.
Frontiers in Plant Science 8: 1347.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2017 | Bielefeld Dissertation | PUB-ID: 2909213
Luhmann N (2017)
Phylogenetic assembly of paleogenomes integrating ancient DNA data.
Bielefeld: Universität Bielefeld.
PUB | PDF
 
2017 | Journal Article | PUB-ID: 2915619
Romanova N, Noll T (2017)
Engineered and Natural Promoters and Chromatin-Modifying Elements for Recombinant Protein Expression in CHO Cells.
Biotechnology Journal 13(3): 1700232.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2911903
Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Sörensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ (2017)
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.
Nature Communications 8: 15708.
PUB | DOI | WoS | PubMed | Europe PMC | NCBI BioProject
 
2017 | Journal Article | PUB-ID: 2906606
Fernandes de Brito L, Irla M, Walter T, Wendisch VF (2017)
Magnesium-aminoclay-based transformation of Paenibacillus riograndensis and Paenibacillus polymyxa and development of tools for gene expression.
Applied Microbiology and Biotechnology 101(2): 735-747.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2912492
Luhmann N, Dörr D, Chauve C (2017)
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.
Microbial Genomics 3(9).
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2918206
Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2017)
Streptomyces ciscaucasicus Sveshnikova et al. 1983 is a later subjective synonym of Streptomyces canus Heinemann et al. 1953.
International Journal of Systematic and Evolutionary Microbiology 68(1): 42-46.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2910380
Hamed A, Abdel-Razek AS, Frese M, Wibberg D, El-Haddad AF, Ibrahim TMA, Kalinowski J, Sewald N, Shaaban M (2017)
New oxaphenalene derivative from marine-derived Streptomyces griseorubens sp ASMR4.
Zeitschrift für Naturforschung B 72(1): 53-62.
PUB | DOI | WoS
 
2017 | Book Chapter | PUB-ID: 2737207
Wendisch VF (2017)
Microbial production of amino acid-related compounds.
In: Amino Acids Fermentation. Yokota A, Ikeda M (Eds); Advances in Biochemical Engineering/Biotechnology, 159. 1st ed. Tokyo: Springer Japan KK: 255-272.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2901460
Löwes B, Chauve C, Ponty Y, Giegerich R (2017)
The BRaliBase Dent – a Tale of Benchmark Design and Interpretation.
Briefings in Bioinformatics 18(2): 306-311.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | 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 (2017)
Corynebacterium glutamicum chassis C1*: Building and testing a novel platform host for synthetic biology and industrial biotechnology.
ACS Synthetic Biology.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2917180
Saad S, Bhatnagar S, Tegetmeyer H, Geelhoed JS, Strous M, Ruff SE (2017)
Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.
ENVIRONMENTAL MICROBIOLOGY 19(12): 4866-4881.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2916929
Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A (2017)
Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.
Microbial Biotechnology.
PUB | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2915890
Huang L, Krüger J, Sczyrba A (2017)
Analyzing large scale genomic data on the cloud with Sparkhit.
Bioinformatics: btx808.
PUB | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2916403
Hossain MS, Persicke M, ElSayed AI, Kalinowski J, Dietz K-J (2017)
Metabolite profiling at the cellular and subcellular level reveals metabolites associated with salinity tolerance in sugar beet.
Journal of Experimental Botany 68(21-22): 5961-5976.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Book Chapter | PUB-ID: 2916878
Mussgnug JH (2017)
Nuclear transformation and toolbox development.
In: Chlamydomonas: Molecular Genetics and Physiology. Hippler M (Ed); Microbiology Monographs, 30. 1st ed. Springer International Publishing: 27-58.
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2914537
Kalinowski J, Ahrens B, Al-Dilaimi A, Winkler A, Wibberg D, Schleenbecker U, Rückert C, Wölfel R, Grass G (2017)
Isolation and whole genome analysis of endospore-forming bacteria from heroin.
Forensic Sci Int Genet 32: 1-6.
PUB | DOI | WoS | PubMed | Europe PMC
 

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