kubasawicki.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Excited to share our new paper in BMC Bioinformatics! We present RSCUcaller, a user-friendly R package to analyze synonymous codon usage bias. It's a versatile tool for genomics & molecular biology research. #RStats #Bioinformatics #CodonUsage bmcbioinformatics.biomedcentral.com/articles/10....

submitted 3 days ago • 0 comments

Got a chance to take the @nanoporetech.com hyp(er accuracy) model for a spin. Pretty decent improvement in read quality 🚀 but expect to spend quite some more GPU hours 😉 (Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)

submitted 15 days ago • 3 comments

New paper in Cladistics explores the tricky phylogeny of feather grasses (Stipeae) using mitochondrial genomes.The study features the first fully assembled mitogenome in the tribe using @nanoporetech.com sequencing: #Botany #UWM onlinelibrary.wiley.com/doi/10.1111/...

submitted 21 days ago • 0 comments

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions. Out now in Current Biology: www.cell.com/current-biol...

submitted 78 days ago • 1 comment

Engineering resistance with help from Liverworts, Mosses and Ferns @Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...

submitted 87 days ago • 0 comments

The first run of @nanoporetech.com RNA004 in our lab. Big leap forward in quality and output. The times like this I wish we have Promethion24 and run all 8 flow cells in parallel. #liverworts #epitranscriptomics #Apopellia

submitted 102 days ago • 1 comment

Elsevier products: ScienceDirect, Scopus, Mendeley, SciVal, SSRN, Pure, Interfolio. . .and that's not all. "They know what you are working on, they know what you are submitting, they know the results of your peer reviews. They control every part of the process and register every action you take."

submitted 205 days ago • 5 comments

1/6 Super excited to share with you our work on Marchantia intra-specific diversity and pan-genomics, just out @naturegenet.bsky.social www.nature.com/articles/s41... Everything on the discoveries in the thread by @chloe-beaulieu.bsky.social I want to emphasize 5 additional points:

submitted 122 days ago • 3 comments

Sex chromosime evolution in complex thalloid #liverworts from the perspective of #Riccia genomics. Both Riccia genomes were assembled using @nanoporetech.com Pore-C and native DNA sequencing: nph.onlinelibrary.wiley.com/doi/full/10....

submitted 129 days ago • 0 comments

Seriously? 1M$ for Q20 short read machine?

submitted 146 days ago • 0 comments

Huge performance update in today’s dorado v0.9.1 release on Ampere 8.6/8.7 & Ada Lovelace 8.9 nvidia GPUs with up to 2x increase in throughput with hac calling and 3x sup! 🚀 Plus a whole bunch of updates for dorado polish and the odd misc bug fix. github.com/nanoporetech...

submitted 149 days ago • 1 comment

We are pleased to share our work on the evolution of translation initiation now published in Nature Communications. Take a look at leaderless mRNAs and eS26 in the small ribosomal subunit of Saccharolobus solfataricus. rdcu.be/d5pgg

submitted 154 days ago • 0 comments

Mk1 family of @nanoporetech.com sequencers

submitted 149 days ago • 0 comments

New kid on the block 😎 Upgrade of our @nanoporetech.com mk1c

submitted 150 days ago • 0 comments

The first T2T assembly and annotation of #liverwort Riccia sorocarpa genome using only @nanoporetech.com technology. Done using 2 Promethion flow cells and one minion for cDNA sequencing. More to come soon... www.nature.com/articles/s41...

submitted 151 days ago • 2 comments

Some insight into biology and organellar genomics of rare #liverwort Arnellia fennica. Genomic data generates sorely using @nanoporetech.com technology: www.nature.com/articles/s41...

submitted 155 days ago • 0 comments

📜 Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs 🧑‍🔬 @luciaborniego.bsky.social, @msr20.bsky.social, @inneslab.bsky.social, et al. 📔 @pnas.org 🔗 www.pnas.org/doi/10.1073/... #️⃣ #PlantScience #PlantImmunity #PlantRNAs

submitted 155 days ago • 0 comments

Adenine DNA methylation associated to transcription is widespread across eukaryotes prelights.biologists.com/highlights/a...

submitted 156 days ago • 0 comments

grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions https://www.biorxiv.org/content/10.1101/2025.01.09.632104v1

submitted 156 days ago • 0 comments

Dendrograms in ggplot2 heatmaps 🔥 Check out the great `legendry` package by @teunbrand.bsky.social github.com/teunbrand/le...

submitted 158 days ago • 2 comments

New Article: "Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation" rdcu.be/d5Mrn Comprehensive and quantitative mapping of pseudouridine sites across four plant species. #PlantScience

submitted 160 days ago • 1 comment

I wonder if we'll be able to run #dorado @nanoporetech.com basecaller on it: www.nvidia.com/en-us/projec...

submitted 161 days ago • 0 comments

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

submitted 162 days ago • 5 comments

Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1

submitted 164 days ago • 0 comments

ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing https://www.biorxiv.org/content/10.1101/2025.01.04.631307v1

submitted 165 days ago • 0 comments

Really pleased to transition from 2024 to 2025 with Tatiana Vernie's work on the evolution of the common symbiosis pathway published @pnas.org 🔽 We finally demonstrate that ☘️ have maintained a genetic pathway to engage with🍄for half a billion years! www.pnas.org/doi/10.1073/...

submitted 169 days ago • 4 comments

Some insights into Ribes organellar genomics with long-reads @nanoporetech.com assembly using single MinION R10.4.1 flow cell: link.springer.com/article/10.1...

submitted 171 days ago • 0 comments

I'm going to collect and dry some local Radula species ;) nph.onlinelibrary.wiley.com/doi/10.1111/...

submitted 173 days ago • 0 comments

📣 Introducing 📣 microPublications in Ecology and Evolution! Please help support this effort by spreading the word and submitting and reviewing papers! #evolution 🌎 🌍 🌏 🧪 #PlantScience #conservation

submitted 430 days ago • 1 comment

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding https://www.biorxiv.org/content/10.1101/2024.12.20.629807v1

submitted 178 days ago • 0 comments

A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵

submitted 195 days ago • 5 comments

RNAkinet identifies nascent RNA by predicting 5EU metabolically labeled #RNA from raw #nanopore electrical signal. Should allow association of RNA metabolism dynamics with isoform usage, poly(A) tails and native RNA mods. academic.oup.com/nargab/artic...

submitted 207 days ago • 3 comments

Our second paper on hospital wastewater - metagenomics and microbial genomics analysed by @nanoporetech.com R10.4.1 pores: www.sciencedirect.com/science/arti...

submitted 192 days ago • 0 comments

The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plants https://www.biorxiv.org/content/10.1101/2024.12.04.626843v1

submitted 193 days ago • 0 comments

Drafted up a Tidyverse-based workflow for micro-synteny. I think it's basic and still effective(?) Made a figure using hypothetical data. I'd like to try some real data before putting it on my GitHub. If you have a favorite locus for micro-synteny, send me a message. #Genomics #DataVisualization

submitted 194 days ago • 3 comments

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data. #Nanopore #SequencingData #Bioinformatics #Genomics @nanoporetech.com 🧬 🖥️ academic.oup.com/bioinformati...

submitted 196 days ago • 0 comments

Phylogenetic turnover of seed plants 🌱 at a global 🌐 and across phylogenetic scales: www.nature.com/articles/s41...

submitted 200 days ago • 2 comments

NCBI's publicly available eukaryotic genome annotation tool, EGAPx: now using orthology and well-supported proteins to classify and name genes, automatic configure based on the species taxon, etc. 🧬🖥️🧪

submitted 198 days ago • 0 comments

Also pumped mPCRselect is out! Work was co-led by @elliecat.bsky.social & former undergrad Julie, we added sims from our tech Tessa, & software updates from Michael. mPCRselect can take a VCF & conduct marker selection for indiv. ID and pop assignment onlinelibrary.wiley.com/doi/10.1111/...

submitted 200 days ago • 0 comments

Exciting news! The latest hifiasm release from Haoyu Cheng and Heng Li adds beta support for @nanoporetech.com simplex R10 reads. Initial results look very promising. 🚀 Check it out: github.com/chhylp123/hi...

submitted 203 days ago • 0 comments