PUB - Publikationen an der Universität Bielefeld

Aging and neurodegeneration are associated with increased mutations in single human neurons.
Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CA., Science 359(6375), 2018
PMID: 29217584

Single-cell metagenomics: challenges and applications.
Xu Y, Zhao F., Protein Cell 9(5), 2018
PMID: 29696589

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.
Zhong ZP, Solonenko NE, Gazitúa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG, Sullivan MB., Front Microbiol 9(), 2018
PMID: 29910780

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.
Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J., Microbiome 6(1), 2018
PMID: 30266101

Viable cyanobacteria in the deep continental subsurface.
Puente-Sánchez F, Arce-Rodríguez A, Oggerin M, García-Villadangos M, Moreno-Paz M, Blanco Y, Rodríguez N, Bird L, Lincoln SA, Tornos F, Prieto-Ballesteros O, Freeman KH, Pieper DH, Timmis KN, Amils R, Parro V., Proc Natl Acad Sci U S A 115(42), 2018
PMID: 30275328

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.
Zhang Q, Wang T, Zhou Q, Zhang P, Gong Y, Gou H, Xu J, Ma B., Sci Rep 7(), 2017
PMID: 28112223

SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions.
Maruyama T, Mori T, Yamagishi K, Takeyama H., BMC Bioinformatics 18(1), 2017
PMID: 28259144

Novel approaches in function-driven single-cell genomics.
Doud DFR, Woyke T., FEMS Microbiol Rev 41(4), 2017
PMID: 28591840

Single-cell genomics for the masses.
Tringe SG., Nat Biotechnol 35(7), 2017
PMID: 28700562

Template-dependent multiple displacement amplification for profiling human circulating RNA.
Wang W, Ren Y, Lu Y, Xu Y, Crosby SD, Di Bisceglie AM, Fan X., Biotechniques 63(1), 2017
PMID: 28701144

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.
Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR., Elife 6(), 2017
PMID: 28678007

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.
Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A., Nat Commun 8(1), 2017
PMID: 28729688

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T., Nat Biotechnol 35(8), 2017
PMID: 28787424

Pleomorphic bacteria-like structures in human blood represent non-living membrane vesicles and protein particles.
Martel J, Wu CY, Huang PR, Cheng WY, Young JD., Sci Rep 7(1), 2017
PMID: 28878382

Challenging a bioinformatic tool's ability to detect microbial contaminants using in silico whole genome sequencing data.
Olson ND, Zook JM, Morrow JB, Lin NJ., PeerJ 5(), 2017
PMID: 28924496

Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level.
Chen Z, Chen L, Zhang W., Front Microbiol 8(), 2017
PMID: 28979258

High-Resolution Single-Cell Sequencing of Malaria Parasites.
Trevino SG, Nkhoma SC, Nair S, Daniel BJ, Moncada K, Khoswe S, Banda RL, Nosten F, Cheeseman IH., Genome Biol Evol 9(12), 2017
PMID: 29220419

ProDeGe: a computational protocol for fully automated decontamination of genomes.
Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, Dangl JL, Ivanova N, Woyke T, Kyrpides N, Pati A., ISME J 10(1), 2016
PMID: 26057843

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes.
Kolinko S, Richter M, Glöckner FO, Brachmann A, Schüler D., Environ Microbiol 18(1), 2016
PMID: 26060021

Viral metagenomics applied to blood donors and recipients at high risk for blood-borne infections.
Sauvage V, Laperche S, Cheval J, Muth E, Dubois M, Boizeau L, Hébert C, Lionnet F, Lefrère JJ, Eloit M., Blood Transfus 14(5), 2016
PMID: 27136432

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples.
Rhee M, Light YK, Meagher RJ, Singh AK., PLoS One 11(5), 2016
PMID: 27144304

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model.
Hu J, Raikhel V, Gopalakrishnan K, Fernandez-Hernandez H, Lambertini L, Manservisi F, Falcioni L, Bua L, Belpoggi F, L Teitelbaum S, Chen J., Microbiome 4(1), 2016
PMID: 27301250

Virtual microfluidics for digital quantification and single-cell sequencing.
Xu L, Brito IL, Alm EJ, Blainey PC., Nat Methods 13(9), 2016
PMID: 27479330

Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens.
Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA., Front Microbiol 7(), 2016
PMID: 27667984

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.
Rinke C, Low S, Woodcroft BJ, Raina JB, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P., PeerJ 4(), 2016
PMID: 27688978

acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.
Lux M, Krüger J, Rinke C, Maus I, Schlüter A, Woyke T, Sczyrba A, Hammer B., BMC Bioinformatics 17(1), 2016
PMID: 27998267

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity.
Davison M, Hall E, Zare R, Bhaya D., Photosynth Res 126(1), 2015
PMID: 25515769

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal.
Konstantinidis KT, Rosselló-Móra R., Syst Appl Microbiol 38(4), 2015
PMID: 25681255

Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems.
Scott JJ, Breier JA, Luther GW, Emerson D., PLoS One 10(3), 2015
PMID: 25760332

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.
Tamminen MV, Virta MP., Front Microbiol 6(), 2015
PMID: 25814987

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount.
Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D., ISME J 9(4), 2015
PMID: 25303714

The changing landscape of microbial biodiversity exploration and its implications for systematics.
Hedlund BP, Dodsworth JA, Staley JT., Syst Appl Microbiol 38(4), 2015
PMID: 25921438

The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign.
Salcher MM, Neuenschwander SM, Posch T, Pernthaler J., ISME J 9(11), 2015
PMID: 25942006

A transcription and translation-coupled DNA replication system using rolling-circle replication.
Sakatani Y, Ichihashi N, Kazuta Y, Yomo T., Sci Rep 5(), 2015
PMID: 26013404

Whole-Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample.
Han HS, Cantalupo PG, Rotem A, Cockrell SK, Carbonnaux M, Pipas JM, Weitz DA., Angew Chem Int Ed Engl 54(47), 2015
PMID: 26316088

Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.
Nishikawa Y, Hosokawa M, Maruyama T, Yamagishi K, Mori T, Takeyama H., PLoS One 10(9), 2015
PMID: 26389587

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays.
Morinishi LS, Blainey P., J Vis Exp (103), 2015
PMID: 26436576

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses.
Weinmaier T, Probst AJ, La Duc MT, Ciobanu D, Cheng JF, Ivanova N, Rattei T, Vaishampayan P., Microbiome 3(), 2015
PMID: 26642878

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi.
Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L., ISME J 8(2), 2014
PMID: 23966099

Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community.
Shintani M, Matsui K, Inoue J, Hosoyama A, Ohji S, Yamazoe A, Nojiri H, Kimbara K, Ohkuma M., Appl Environ Microbiol 80(1), 2014
PMID: 24141122

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms.
Goffredi SK, Yi H, Zhang Q, Klann JE, Struve IA, Vrijenhoek RC, Brown CT., ISME J 8(4), 2014
PMID: 24225886

Marine viruses, a genetic reservoir revealed by targeted viromics.
Martínez Martínez J, Swan BK, Wilson WH., ISME J 8(5), 2014
PMID: 24304671

Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer.
Wilkins MJ, Kennedy DW, Castelle CJ, Field EK, Stepanauskas R, Fredrickson JK, Konopka AE., Microbiology 160(pt 2), 2014
PMID: 24324032

Bacterial vesicles in marine ecosystems.
Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW., Science 343(6167), 2014
PMID: 24408433

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust.
Robador A, Jungbluth SP, LaRowe DE, Bowers RM, Rappé MS, Amend JP, Cowen JP., Front Microbiol 5(), 2014
PMID: 25642212

Preparation of Phi29 DNA polymerase free of amplifiable DNA using ethidium monoazide, an ultraviolet-free light-emitting diode lamp and trehalose.
Takahashi H, Yamazaki H, Akanuma S, Kanahara H, Saito T, Chimuro T, Kobayashi T, Ohtani T, Yamamoto K, Sugiyama S, Kobori T., PLoS One 9(2), 2014
PMID: 24505243

Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes.
Dichosa AE, Daughton AR, Reitenga KG, Fitzsimons MS, Han CS., Nat Protoc 9(3), 2014
PMID: 24525754

Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin.
Kaster AK, Mayer-Blackwell K, Pasarelli B, Spormann AM., ISME J 8(9), 2014
PMID: 24599070

Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW., Science 344(6182), 2014
PMID: 24763590

Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.
Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Dmitrieff E, Malmstrom R, Stepanauskas R, Woyke T., Nat Protoc 9(5), 2014
PMID: 24722403

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.
Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE., PeerJ 2(), 2014
PMID: 24918035

Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate.
Džunková M, Garcia-Garcerà M, Martínez-Priego L, D'Auria G, Calafell F, Moya A., PLoS One 9(6), 2014
PMID: 24887077

Improved multiple displacement amplification (iMDA) and ultraclean reagents.
Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW., BMC Genomics 15(), 2014
PMID: 24906487

Effects of sample treatments on genome recovery via single-cell genomics.
Clingenpeel S, Schwientek P, Hugenholtz P, Woyke T., ISME J 8(12), 2014
PMID: 24926860

Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill.
Mason OU, Han J, Woyke T, Jansson JK., Front Microbiol 5(), 2014
PMID: 25071745

Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter".
Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T., Extremophiles 18(5), 2014
PMID: 25113821

Partition enrichment of nucleotide sequences (PINS)--a generally applicable, sequence based method for enrichment of complex DNA samples.
Kvist T, Sondt-Marcussen L, Mikkelsen MJ., PLoS One 9(9), 2014
PMID: 25203653

Hidden diversity in honey bee gut symbionts detected by single-cell genomics.
Engel P, Stepanauskas R, Moran NA., PLoS Genet 10(9), 2014
PMID: 25210772

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton.
Garcia SL, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F., ISME J 7(1), 2013
PMID: 22810059

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP., Nat Commun 4(), 2013
PMID: 23673639

Optofluidic cell selection from complex microbial communities for single-genome analysis.
Landry ZC, Giovanonni SJ, Quake SR, Blainey PC., Methods Enzymol 531(), 2013
PMID: 24060116

The future is now: single-cell genomics of bacteria and archaea.
Blainey PC., FEMS Microbiol Rev 37(3), 2013
PMID: 23298390

Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park.
Romano C, D'Imperio S, Woyke T, Mavromatis K, Lasken R, Shock EL, McDermott TR., Appl Environ Microbiol 79(9), 2013
PMID: 23435891

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS., Genome Res 23(5), 2013
PMID: 23493677

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS., Genome Res 23(5), 2013
PMID: 23564253

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS., Proc Natl Acad Sci U S A 110(26), 2013
PMID: 23754396

Accelerating plant breeding.
De La Fuente GN, Frei UK, Lübberstedt T., Trends Plant Sci 18(12), 2013
PMID: 24080381

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA., J Comput Biol 20(10), 2013
PMID: 24093227

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes.
Close DW, Ferrara F, Dichosa AE, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury AR., BMC Microbiol 13(), 2013
PMID: 24279426

Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations.
Ellegaard KM, Klasson L, Andersson SG., PLoS One 8(11), 2013
PMID: 24312412

Droplet microfluidics for high-throughput biological assays.
Guo MT, Rotem A, Heyman JA, Weitz DA., Lab Chip 12(12), 2012
PMID: 22318506

SNP array-based copy number and genotype analyses for preimplantation genetic diagnosis of human unbalanced translocations.
van Uum CM, Stevens SJ, Dreesen JC, Drüsedau M, Smeets HJ, Hollanders-Crombach B, Die-Smulders CE, Geraedts JP, Engelen JJ, Coonen E., Eur J Hum Genet 20(9), 2012
PMID: 22378284

Genomic sequencing of uncultured microorganisms from single cells.
Lasken RS., Nat Rev Microbiol 10(9), 2012
PMID: 22890147