Microbial Single Cell Genomics

A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

Biderre-Petit C, Courtine D, Hennequin C, ..., Divne A, Hochart C

Mol Ecol Resour - (-) e13923 [2024-01-08; online 2024-01-08]

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

Year 2023

Single-cell sequencing of tumor-associated macrophages in a Drosophila model.

Khalili D, Mohammed M, Kunc M, ..., Ankarklev J, Theopold U

Front Immunol 14 (-) 1243797 [2023-09-19; online 2023-09-19]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

De novoassembled single-cell transcriptomes from aquatic phytoflagellates reveal a metabolically distinct cell population

Florenza J, Jeevannavar A, Divne AM, Tamminen M, Bertilsson S

- - (-) - [2023-08-31; online 2023-08-31]

Microbial Single Cell Genomics [Technology development]

scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics.

Hildebrandt F, Mohammed M, Dziedziech A, ..., Henriksson J, Ankarklev J

Front Immunol 14 (-) 1224591 [2023-07-27; online 2023-07-27]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.

Mohammed M, Dziedziech A, Sekar V, ..., Vega-Rodriguez J, Ankarklev J

Microbiol Spectr 11 (2) e0367122 [2023-02-27; online 2023-02-27]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Year 2022

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 (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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 Support for Computational Resources [Service] Microbial Single Cell Genomics [Service]

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 Support for Computational Resources [Service] Microbial Single Cell Genomics NGI Single cell [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

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]

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

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

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

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 Support for Computational Resources [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

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]

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

Year 2019

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

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 Support for Computational Resources [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]

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]

Year 2017

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]

Year 2016

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 Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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]

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