Microbial Single Cell Genomics (12 publications)

Publications

SciLifeLab National facility since 2015.

12 publications

Year 2020

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells

Onsbring H, Tice AK, Barton BT, Brown MW, Ettema TJG

BMC Genomics 21 (1) 448 [2020-12-00; online 2020-06-29]

Microbial Single Cell Genomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A

Sci Rep 10 (1) - [2020-12-00; online 2020-01-28]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DOI Crossref

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation

Kwon H, Franzén O, Mohammed M, Ankarklev J, Smith RC

- - (-) - [2020-07-11; online 2020-07-11]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative]

Year 2019

DOI Crossref

Uncovering microbial inter-domain interactions in complex communities

Florenza J, Tamminen M, Bertilsson S

Phil. Trans. R. Soc. B 374 (1786) 20190087 [2019-11-25; online 2019-10-07]

Microbial Single Cell Genomics [Technology development]

Year 2018

PubMed DOI Crossref

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J

BioProject: PRJNA273799 SRA: SRP058493

Microbiome 6 (1) - [2018-12-00; online 2018-09-28]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DOI Crossref

High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force

Deng P, Fu CJ, Wu Z

RSC Adv. 8 (62) 35512-35520 [2018-00-00; online 2018-00-00]

Microbial Single Cell Genomics [Service]

Year 2017

PubMed DOI Crossref

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.

Mußmann M, Pjevac P, Krüger K, Dyksma S

pii: ismej2016185 pmc: PMC5437919

ISME J 11 (5) 1276-1281 [2017-05-00; online 2017-01-06]

Microbial Single Cell Genomics [Service]

Year 2016

PubMed DOI Crossref

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN

pii: 10.1186/s40168-016-0197-7 pmc: PMC5054601

Microbiome 4 (1) 52 [2016-10-06; online 2016-10-06]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.

Eiler A, Mondav R, Sinclair L, ..., Woyke T, Bertilsson S

pii: ismej2015260 pmc: PMC5029164

ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-20]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Microbial Single Cell Genomics [Collaborative]

PubMed DOI Crossref

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Troell K, Hallström B, Divne AM, ..., Beser J, Bertilsson S

pii: 10.1186/s12864-016-2815-y pmc: PMC4917956

BMC Genomics 17 (-) 471 [2016-06-23; online 2016-06-23]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

Baker BJ, Saw JH, Lind AE, ..., Teske AP, Ettema TJG

pii: nmicrobiol20162

Nat Microbiol 1 (-) 16002 [2016-02-15; online 2016-02-15]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2015

PubMed DOI Crossref

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

Saw JH, Spang A, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJG

pii: rstb.2014.0328 pmc: PMC4571567 Dryad: df264

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370 (1678) 20140328 [2015-09-26; online 2015-09-02]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure