Microbial Single Cell Genomics

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SciLifeLab Infrastructure Unit Since 2017.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2017

Ended: Current

Year 2023

PubMed DOI Crossref
Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis.
van Creij J, Auxier B, An J, ..., Pan Z, Limpens E
BMC Genomics 24 (1) 53 [2023-01-28; online 2023-01-28]
Microbial Single Cell Genomics [Service]

Year 2022

PubMed DOI Crossref
Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.
Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A
Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The genomic basis of hybrid male sterility in <i>Ficedula</i> flycatchers
Segami JC, Mugal CF, Cunha C, ..., Semon M, Qvarnström A
- - (-) - [2022-09-19; online 2022-09-19]
Microbial Single Cell Genomics [Service]
PubMed DOI Crossref
Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections.
Rosendal E, Mihai IS, Becker M, ..., Överby AK, Lenman A
MBio 13 (3) e0089222 [2022-06-28; online 2022-05-09]
Affinity Proteomics Uppsala [Service] Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service]
PubMed DOI Crossref
scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.
Raine A, Lundmark A, Annett A, ..., Bergin C, Nordlund J
Sci Rep 12 (1) 5772 [2022-04-06; online 2022-04-06]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics NGI Single cell [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
DOI Crossref
Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity
Garcia SL, Nuy JK, Mehrshad M, ..., Hawkes J, Bertilsson S
- - (-) - [2022-03-22; online 2022-03-22]
Microbial Single Cell Genomics [Technology development]
DOI Crossref
Single-Cell Transcriptomics reveals relaxed evolutionary constraint of spermatogenesis in two passerine birds as compared to mammals
Segami JC, Semon M, Cunha C, ..., Mugal CF, Qvarnström A
- - (-) - [2022-01-23; online 2022-01-23]
Microbial Single Cell Genomics [Technology development]

Year 2021

PubMed DOI Crossref
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.
Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F
Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A
Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]
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]
PubMed DOI Crossref
Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.
Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC
Elife 10 (-) - [2021-07-28; online 2021-07-28]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] Microbial Single Cell Genomics NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2020

PubMed DOI Crossref
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 [2020-06-29; 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) 1303 [2020-01-28; 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]

Year 2019

PubMed DOI Crossref
Uncovering microbial inter-domain interactions in complex communities.
Florenza J, Tamminen M, Bertilsson S
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 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
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
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
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
ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-19]
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
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
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
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

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Publications 9.2.2