2981 Publications

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
 
2017 | Journal Article | PUB-ID: 2914367
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu Y-W, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin H-H, Liao Y-C, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk H-P, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC (2017)
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software.
Nature Methods 14(11): 1063-1071.
PUB | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2907915
Taniguchi H, Henke NA, Heider S, Wendisch VF (2017)
Overexpression of the primary sigma factor gene sigA improved carotenoid production by Corynebacterium glutamicum: application to production of beta-carotene and the non-native linear C50 carotenoid bisanhydrobacterioruberin.
Metabolic Engineering Communications 4: 1-11.
PUB | PDF | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2908419
Torres Tejerizo GA, Wibberg D, Winkler A, Ormeño-Orrillo E, Martínez-Romero E, Niehaus K, Pühler A, Kalinowski J, Lagares A, Schlüter A, Pistorio M (2017)
Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.
Genome Announcements 5(4): e01513-16.
PUB | PDF | DOI
 
2017 | 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 (Accepted)
Invasion ecology applied to inoculation of plant growth promoting bacteria through a novel SIMPER-PCA approach.
Plant and Soil.
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2913556
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, Stoye J (2017)
Bioinformatics for NGS-based metagenomics and the application to biogas research.
Journal of Biotechnology 261(SI): 10-23.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2914662
Fernandes de Brito L, Irla M, Kalinowski J, Wendisch VF (2017)
Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology.
BMC Genomics 18: 846.
PUB | PDF | DOI | PubMed | Europe PMC
 
2017 | Research Data | PUB-ID: 2914921
Huang L, Krüger J, Sczyrba A (2017) : Sparkhit evaluation data set. Bielefeld University. doi:10.4119/unibi/2914921.
PUB | Files available | DOI
 
2017 | Journal Article | PUB-ID: 2910629
Perez F, Ziert C, Risse JM, Wendisch VF (2017)
Improved fermentative production of the compatible solute ectoine by Corynebacterium glutamicum from glucose and alternative carbon sources.
J Biotechnol 258: 59-68.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2908307
Perez F, Risse JM, Friehs K, Wendisch VF (2017)
Fermentative production of L-pipecolic acid from glucose and alternative carbon sources.
Biotechnology Journal 12(7): 1600646.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2914868
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R, Rivera JLA, Al-Moosawi L, Alverdy J, Amato KR, Andras J, Angenent LT, Antonopoulos DA, Apprill A, Armitage D, Ballantine K, Bárta Jˇí, Baum JK, Berry A, Bhatnagar A, Bhatnagar M, Biddle JF, Bittner L, Boldgiv B, Bottos E, Boyer DM, Braun J, Brazelton W, Brearley FQ, Campbell AH, Caporaso JG, Cardona C, Carroll JL, Cary SC, Casper BB, Charles TC, Chu H, Claar DC, Clark RG, Clayton JB, Clemente JC, Cochran A, Coleman ML, Collins G, Colwell RR, Contreras M, Crary BB, Creer S, Cristol DA, Crump BC, Cui D, Daly SE, Davalos L, Dawson RD, Defazio J, Delsuc F, Dionisi HM, Dominguez-Bello MG, Dowell R, Dubinsky EA, Dunn PO, Ercolini D, Espinoza RE, Ezenwa V, Fenner N, Findlay HS, Fleming ID, Fogliano V, Forsman A, Freeman C, Friedman ES, Galindo G, Garcia L, Garcia-Amado MA, Garshelis D, Gasser RB, Gerdts G, Gibson MK, Gifford I, Gill RT, Giray T, Gittel A, Golyshin P, Gong D, Grossart H-P, Guyton K, Haig S-J, Hale V, Hall RS, Hallam SJ, Handley KM, Hasan NA, Haydon SR, Hickman JE, Hidalgo G, Hofmockel KS, Hooker J, Hulth S, Hultman J, Hyde E, Ibáñez-Álamo JD, Jastrow JD, Jex AR, Johnson LS, Johnston ER, Joseph S, Jurburg SD, Jurelevicius D, Karlsson A, Karlsson R, Kauppinen S, Kellogg CTE, Kennedy SJ, Kerkhof LJ, King GM, Kling GW, Koehler AV, Krezalek M, Kueneman J, Lamendella R, Landon EM, Lane-deGraaf K, LaRoche J, Larsen P, Laverock B, Lax S, Lentino M, Levin II, Liancourt P, Liang W, Linz AM, Lipson DA, Liu Y, Lladser ME, Lozada M, Spirito CM, MacCormack WP, MacRae-Crerar A, Magris M, Martín-Platero AM, Martín-Vivaldi M, Martínez LM, Martínez-Bueno M, Marzinelli EM, Mason OU, Mayer GD, McDevitt-Irwin JM, McDonald JE, McGuire KL, McMahon KD, McMinds R, Medina M, Mendelson JR, Metcalf JL, Meyer F, Michelangeli F, Miller K, Mills DA, Minich J, Mocali S, Moitinho-Silva L, Moore A, Morgan-Kiss RM, Munroe P, Myrold D, Neufeld JD, Ni Y, Nicol GW, Nielsen S, Nissimov JI, Niu K, Nolan MJ, Noyce K, O’Brien SL, Okamoto N, Orlando L, Castellano YO, Osuolale O, Oswald W, Parnell J, Peralta-Sánchez JM, Petraitis P, Pfister C, Pilon-Smits E, Piombino P, Pointing SB, Pollock FJ, Potter C, Prithiviraj B, Quince C, Rani A, Ranjan R, Rao S, Rees AP, Richardson M, Riebesell U, Robinson C, Rockne KJ, Rodriguezl SM, Rohwer F, Roundstone W, Safran RJ, Sangwan N, Sanz V, Schrenk M, Schrenzel MD, Scott NM, Seger RL, Seguin-Orlando A, Seldin L, Seyler LM, Shakhsheer B, Sheets GM, Shen C, Shi Y, Shin H, Shogan BD, Shutler D, Siegel J, Simmons S, Sjöling S, Smith DP, Soler JJ, Sperling M, Steinberg PD, Stephens B, Stevens MA, Taghavi S, Tai V, Tait K, Tan CL, Tas¸ N, Taylor DL, Thomas T, Timling I, Turner BL, Urich T, Ursell LK, van der Lelie D, Van Treuren W, van Zwieten L, Vargas-Robles D, Thurber RV, Vitaglione P, Walker DA, Walters WA, Wang S, Wang T, Weaver T, Webster NS, Wehrle B, Weisenhorn P, Weiss S, Werner JJ, West K, Whitehead A, Whitehead SR, Whittingham LA, Willerslev E, Williams AE, Wood SA, Woodhams DC, Yang Y, Zaneveld J, Zarraonaindia I, Zhang Q, Zhao H (2017)
A communal catalogue reveals Earth’s multiscale microbial diversity.
Nature.
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2910249
Jaeger D, Hübner W, Huser T, Mussgnug JH, Kruse O (2017)
Nuclear transformation and functional gene expression in the oleaginous microalga Monoraphidium neglectum.
Journal of Biotechnology 249: 10-15.
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2913386
Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O (2017)
Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation.
Biotechnology for Biofuels 10: 197.
PUB | PDF | DOI
 
2017 | Journal Article | PUB-ID: 2910571
Jorge J, Perez F, Wendisch VF (2017)
A new metabolic route for the fermentative production of 5-aminovalerate from glucose and alternative carbon sources.
Bioresource Technology 245: 1701–1709.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2911321
Lee J-H, Wendisch VF (2017)
Production of amino acids - Genetic and metabolic engineering approaches.
Biores Technol 245: 1575–1587.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913472
Rodríguez-Castillo JG, Pino C, Niño LF, Rozo JC, Llerena-Polo C, Parra-López CA, Tauch A, Murcia-Aranguren MI (2017)
Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance.
Infect Genet Evol 54: 314-323.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913749
Sant'Anna F, Ambrosini A, de Souza R, Fernandes GD, Bach E, Balsanelli E, Baura V, Fernandes de Brito L, Wendisch VF, de Oliveira Pedrosa F, de Souza EM, Passaglia L (2017)
Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: genome-based metrics improve bacterial taxonomic classification.
Front. Microbiol. 8: 1849.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913898
Wendisch VF (2017)
Journal Club: Calvin-Zyklus-Enzym reguliert Methanol-Stoffwechsel.
BIOspektrum 06.17: 666.
PUB
 
2017 | Journal Article | PUB-ID: 2914538
Ortseifen V, Kalinowski J, Pühler A, Rückert C (2017)
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.
J Biotechnol.
PUB | DOI | PubMed | Europe PMC
 
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 | PubMed | Europe PMC
 
2017 | Conference Paper | PUB-ID: 2909409
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.
In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
PUB | DOI
 
2017 | Conference Paper | PUB-ID: 2907587
Holley G, Wittler R, Stoye J, Hach F (2017)
Dynamic Alignment-Free and Reference-Free Read Compression.
In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
PUB | DOI
 
2017 | Conference Paper | PUB-ID: 2913015
Rubert DP, Medeiros GL, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2017)
Algorithms for Computing the Family-Free Genomic Similarity under DCJ.
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 10562. Springer Verlag: 76-100.
PUB | DOI
 
2017 | Conference Paper | PUB-ID: 2913016
Schulz T, Stoye J, Dörr D (2017)
Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery.
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
PUB | DOI
 
2017 | Book Chapter | PUB-ID: 2913921
Zekic T, Holley G, Stoye J (In Press)
Pan-genome Storage and Analysis Techniques.
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
2017 | Book Chapter | PUB-ID: 2913922
Dörr D, Feijão P, Stoye J (In Press)
Family-Free Genome Comparison.
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
2017 | Book (Editor) | PUB-ID: 2913920
Setubal JC, Stadler P, Stoye J (Eds) (In Press)
Comparative Genomics: Methods and Protocols. Methods in Molecular Biology; 1704.
Springer Verlag.
PUB
 
2017 | Journal Article | PUB-ID: 2909057
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Approximating the DCJ distance of balanced genomes in linear time.
Algorithms for Molecular Biology 12: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2914105
Schatschneider S, Schneider J, Blom J, Letisse F, Niehaus K, Goesmann A, Vorhölter F-J (2017)
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
MICROBIOLOGY-SGM 163(8): 1117-1144.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913401
Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2017)
Streptomyces phaeopurpureus Shinobu 1957 (Approved Lists 1980) and Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980) are heterotypic subjective synonyms.
International Journal of Systematic and Evolutionary Microbiology.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2914045
Wippermann A, Noll T (2017)
DNA methylation in CHO cells.
Journal of Biotechnology 258: 206-210.
PUB | DOI
 
2017 | Journal Article | PUB-ID: 2906790
Lee J-H, Wendisch VF (2017)
Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass.
J Biotechnol 257: 211-221.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913406
Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J (2017)
Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum.
Journal of Biotechnology 257: 99-109.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2907317
Freyre-González JA, Tauch A (2017)
Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: Novel insights from a dataset with a high genomic coverage.
Journal of Biotechnology 257: 199-210.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913403
Jahn L, Schafhauser T, Wibberg D, Rückert C, Winkler A, Kulik A, Weber T, Flor L, van Pée K-H, Kalinowski J, Ludwig-Müller J, Wohlleben W (2017)
Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin.
Journal of Biotechnology 257: 233-239.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913963
Ruwe M, Kalinowski J, Persicke M (2017)
Identification and Functional Characterization of Small Alarmone Synthetases in Corynebacterium glutamicum.
Frontiers in Microbiology 8: 1601.
PUB | PDF | DOI
 
2017 | Book Chapter | PUB-ID: 2913924
Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (In Press)
Comparative Methods for Reconstructing Ancient Genome Organization.
In: Comparative Genomics. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, Springer Verlag.
PUB
 
2017 | Conference Paper | PUB-ID: 2913690
Zhu L, Ester M (2017)
Bayesian Collective Markov Random Fields for Subcellular Localization Prediction of Human Proteins.
In: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17. ACM Press.
PUB | PDF | DOI
 
2017 | Journal Article | PUB-ID: 2909153
Yu J, Blom J, Sczyrba A, Goesmann A (2017)
Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.
Journal of Biotechnology 257: 58-60.
PUB | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913019
Farnberger JE, Lorenz E, Richter N, Wendisch VF, Kroutil W (2017)
In vivo Plug-and-play: A Modular Multi-enzyme Single-cell Catalyst for the Asymmetric Amination of Ketoacids and Ketones.
Microbial Cell Factories 16: 132.
PUB | DOI | WoS | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2907021
Irla M, Naerdal I, Brautaset T, Wendisch VF (2017)
Methanol-based γ-aminobutyric acid (GABA) production by genetically engineered Bacillus methanolicus strains.
Industrial Crops and Products 106: 12-20.
PUB | DOI | WoS
 
2017 | Journal Article | PUB-ID: 2909055
Pfeifenschneider J, Brautaset T, Wendisch VF (2017)
Methanol as carbon source in the bio-economy: Metabolic engineering of aerobic methylotrophic bacteria for production of value-added chemicals.
Biofuels, Bioproducts and Biorefining 11: 719-731.
PUB | DOI | WoS
 
2017 | Journal Article | PUB-ID: 2913400
Nouioui I, Rückert C, Willemse J, van Wezel GP, Klenk H-P, Busche T, Kalinowski J, Bredholt H, Zotchev SB (2017)
Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.
Antonie Van Leeuwenhoek. Journal of Microbiology.
PUB | DOI | PubMed | Europe PMC
 
2017 | Journal Article | PUB-ID: 2913404
Grimm I, Dumke J, Vollmer T, Hinse D, Rückert C, Kalinowski J, Knabbe C, Dreier J (2017)
Complete Genome Sequence of the Streptococcus gallolyticus subsp. gallolyticus Strain DSM 16831.
Genome Announcements 5(16).
PUB | DOI | 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 | PubMed | Europe PMC
 
2017 | Book Chapter | PUB-ID: 2905383
Heider S, Henke NA, Peters-Wendisch P, Wendisch VF (2017)
C50 carotenoids: Occurrence, biosynthesis, glycosylation and metabolic engineering for their overproduction.
In: Bio-pigmentation and Biotechnology implications. Singh OV (Ed); Hoboken, NJ, USA: John Wiley & Sons, Inc.: 107-126.
PUB
 
2017 | Journal Article | PUB-ID: 2913038
Klassen V, Blifernez-Klassen O, Wibberg D, Winkler A, Kalinowski J, Posten C, Kruse O (2017)
Highly efficient methane generation from untreated microalgae biomass.
Biotechnology for Biofuels 10(1): 186.
PUB | PDF | DOI
 
2017 | Journal Article | PUB-ID: 2912905
Uhmeyer A, Cecchin M, Ballottari M, Wobbe L (2017)
Impaired Mitochondrial Transcription Termination Disrupts the Stromal Redox Poise in Chlamydomonas.
Plant Physiol 174(3): 1399-1419.
PUB | DOI | PubMed | Europe PMC
 
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
 
2017 | Journal Article | PUB-ID: 2913154
Jaen KE, Sigala J-C, Olivares-Hernandez R, Niehaus K, Lara AR (2017)
Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli.
BMC BIOTECHNOLOGY 17: 60.
PUB | DOI | WoS | PubMed | Europe PMC
 

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