New preprint from the group!
Here we use Nanopore dRNA and Ribo-Seq data from multiple yeast species to discover tens of highly conserved microproteins encoded by uORFs in polycistronic transcripts/alternative isoforms. @prbb.org @grib-barcelona.bsky.social
www.biorxiv.org/content/10.6...
At the OHSU School of Dentistry AI in Research Symposium, I presented that AI is a major driver of advances in third-generation sequencing technologies (e.g., Nanopore and PacBio). Our lab is using Nanopore sequencing to study DNA and RNA modifications in oral bacteria. #microbiology #dentistry
Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...
A webpage section listing three resources related to measles virus genomic epidemiology. The first item shows an icon and the heading ‘Measles virus genomic epidemiology’ with a subheading ‘A primer on measles virus genomic epidemiology and why we do it.’ The second item shows an icon and the heading ‘artic-measles/400/v1.0.0 Primer Scheme’ with a description of the ARTIC-network primer scheme for sequencing measles virus. The third item shows an icon and the heading ‘ARTIC-network MEV wet-lab protocol’ with a description of the wet-lab protocol for sequencing MEV using the artic-measles/400/v1.0.0 primer scheme.
A webpage section titled ‘User‑interface pipelines using Epi2me,’ displaying four items. The first item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME’ and describes using EPI2ME to run the ARTIC amplicon‑nf pipeline without the command line. The second item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Illumina Data,’ again describing use of EPI2ME to run the amplicon‑nf pipeline without the command line. The third item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Oxford Nanopore Data,’ with the same description. The fourth item shows an icon with the heading ‘amplicon‑nf: Viewing outputs of the pipeline in EPI2ME,’ describing how to view outputs of the amplicon‑nf pipeline within EPI2ME.
A webpage section titled ‘Command line interface pipeline SOPs.’ The first item shows an icon with the heading ‘Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP’ and labels indicating ‘Nanopore | bioinformatics.’ A second section titled ‘Phylogenetics and Interpretation’ includes an icon with the heading ‘MeV Phylogenetics’ and a description stating it contains resources and protocols for measles virus alignment and phylogenetics.
ARTIC 2 measles resources are live!
As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics
📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
www.doi.org/10.1099/mgen.0.001644
🖥️🧬💻
#AcademicSky
#MicroSky
#IDSky
🧪🧫🦠
Happy our preprint is out🦠:
"Evaluation of an Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT culture"
We developed and tested a workflow for long-read sequencing of #mycobacteria, including optimising DNA extraction and assessing how #ONT performs compared with #Illumina.
"Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease."
www.biorxiv.org/content/10.6...
Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome
www.nature.com/articles/s41...
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
End of an era! 🧬 Our latest paper is out now in Microbiology Spectrum.
This marks our final study utilizing the @nanoporetech.com RNA002 chemistry before we transition to RNA004. It’s been a wild ride with those flow cells! 🧪📖
Read it here: journals.asm.org/doi/10.1128/...
#Nanopore #DRS #UWM
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT.
www.sciencedirect.com/science/arti...
🧵1/7
🧪
We are on!
Air 🌬️
Sea spray 💦
Surface 🌊
3000 m deep ⚓
~1 million DNA molecules/hour
sequenced live in the middle of the Pacific Ocean!
Shout out to Aden and Rhonda,l who can extract DNA, PCR, and library prep without getting seasick ⛵️
From sample to data in less than 48 hrs.
#eDNA #nanopore #UW
Genotypic Technology invites you to an exclusive webinar on Oxford Nanopore RNA Sequencing, exploring how long-read and direct RNA sequencing overcome the limitations of short-read platforms.
Register now shorturl.at/uCc1Q
Need an excuse to visit Antwerp in April? You can register for our Flanders Nanopore Day. Research using @nanoporetech.com sequencing will be highlighted, throughout a variety of research fields. And for academia, registration is for free.
nanoporeflanders.be
@keygene.com 's @awngs.bsky.social will be a speaker during the Industry Workshop of Oxford Nanopore Technologies ( @nanoporetech.com ), presenting some recent results in technology development for single-nuclei transcriptomics at PAG33 in San Diego on January 12.
Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10....
Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!
Long-read Nanopore WGS can resolve large multi-kb integration events in HPV infected cells, that cause structural rearrangements, leading to oncogenesis.
A new study shows MTB surveillance and transmission can be resolved without culture or capture-based enrichment, using nanopore WGS directly from sputum.
www.biorxiv.org/content/10.1...
Long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients; authors were able to identify differences in splice isoforms for genes that modulate immune signaling and apoptosis.
Interesting news in the world of transposable elements. Discovery of "a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active" in Paramecium aurelia.
www.biorxiv.org/content/10.1...
Long-read de novo assemblies for 5 paracoccidioides fungal pathogen species endemic to Latin America. (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis and P. lutzii)
www.biorxiv.org/content/10.1...
"This work validates ONT long-read sequencing as a powerful tool for marine microbiome studies to catalyze advancements in the fields of ecology and evolution, resource management, and conservation"
www.biorxiv.org/content/10.1...
Very cool to see the early results of nanopore sequencing of PEPTIDES!
The ability to perform genomics, transcriptomics and proteomics on a single platform is incredibly exciting, and the potential for future applications is massive.
www.biorxiv.org/content/10.1...
Not sure which tick reference genome to use for your analysis?
This paper provides a very nice assessment of 34 high-quality tick genome assemblies from 21 species.
www.biorxiv.org/content/10.1...
Using long reads that can span the length of telomeric regions, researchers developed a method to measure telomere length in S. cerevisiae, and found wide variation in telomere length, ploidy, and subtelomere structure.
buff.ly/hGM08qS
Long-read WGS of 48 L. infantum identified drug-resistance biomarkers in 80% of the isolates!
"Leveraging WGS, our approach provides a methodological advantage by complementing CNV analysis with detailed read sequence profiling "
buff.ly/LRIDrOr
Potentially useful new tool for targeted microbial genomics.
- Toolkit to design selective WGA (sWGA) primers
- ~99% on-target reads + strong genome coverage when tested with P. falciparum samples
- Validated with long read Oxofrd Nanopore sequencing
🧬 Now published in Bioinformatics Advances: "Snappy: Fast identification of DNA methylation motifs based on Oxford Nanopore reads"
Full article available: https://doi.org/10.1093/bioadv/vbaf296
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
