Kuba Sawicki
@kubasawicki.bsky.social
Bryologist, UWM Sequencing Core Lab
Researcher at Department of Botany and Evolutionary Ecology, University of Warmia and Mazury in Olsztyn, Poland
Researcher at Department of Botany and Evolutionary Ecology, University of Warmia and Mazury in Olsztyn, Poland
Our latest study reveals how RNA modifications (m⁶A, m⁵C, and pseudouridine) shape the environmental adaptation of the amphibious liverwort Riccia fluitans. 🌿💧
Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome.
#UMW #Riccia
📄 Read here: www.sciencedirect.com/science/arti...
Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome.
#UMW #Riccia
📄 Read here: www.sciencedirect.com/science/arti...
Epitranscriptomic and expression profiling in Riccia fluitans across diverse environmental conditions
Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), are critical regulators of pl…
www.sciencedirect.com
October 4, 2025 at 6:35 PM
Our latest study reveals how RNA modifications (m⁶A, m⁵C, and pseudouridine) shape the environmental adaptation of the amphibious liverwort Riccia fluitans. 🌿💧
Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome.
#UMW #Riccia
📄 Read here: www.sciencedirect.com/science/arti...
Using direct RNA @nanoporetech.com sequencing, SBS RNAseq and metabolome.
#UMW #Riccia
📄 Read here: www.sciencedirect.com/science/arti...
Reposted by Kuba Sawicki
NEW ARTICLE FROM THE LAB 🎉🍀🧫
Groundbreaking work performed by @hueihsuantsai.bsky.social and all!
Please, go have a read! Congrats to making it to the cover!!!
www.science.org/doi/10.1126/...
Groundbreaking work performed by @hueihsuantsai.bsky.social and all!
Please, go have a read! Congrats to making it to the cover!!!
www.science.org/doi/10.1126/...
October 2, 2025 at 6:09 PM
NEW ARTICLE FROM THE LAB 🎉🍀🧫
Groundbreaking work performed by @hueihsuantsai.bsky.social and all!
Please, go have a read! Congrats to making it to the cover!!!
www.science.org/doi/10.1126/...
Groundbreaking work performed by @hueihsuantsai.bsky.social and all!
Please, go have a read! Congrats to making it to the cover!!!
www.science.org/doi/10.1126/...
We just published TAILcaller 🧬 — an R package for analyzing poly(A) tail length directly from @nanoporetech.com Dorado BAMs.
✅ Works with dRNA & cDNA
✅ PCA, volcano/MA plots, heatmaps
✅ Adaptive tests beyond Wilcoxon
Case studies: 🌱 Riccia fluitans
#liverworts #UWM
academic.oup.com/bioinformati...
✅ Works with dRNA & cDNA
✅ PCA, volcano/MA plots, heatmaps
✅ Adaptive tests beyond Wilcoxon
Case studies: 🌱 Riccia fluitans
#liverworts #UWM
academic.oup.com/bioinformati...
TAILcaller: an R package for analyzing differences in poly(A) tail length for Oxford Nanopore RNA sequencing
AbstractMotivation. Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of t
academic.oup.com
September 28, 2025 at 7:36 PM
We just published TAILcaller 🧬 — an R package for analyzing poly(A) tail length directly from @nanoporetech.com Dorado BAMs.
✅ Works with dRNA & cDNA
✅ PCA, volcano/MA plots, heatmaps
✅ Adaptive tests beyond Wilcoxon
Case studies: 🌱 Riccia fluitans
#liverworts #UWM
academic.oup.com/bioinformati...
✅ Works with dRNA & cDNA
✅ PCA, volcano/MA plots, heatmaps
✅ Adaptive tests beyond Wilcoxon
Case studies: 🌱 Riccia fluitans
#liverworts #UWM
academic.oup.com/bioinformati...
Our new study on the liverwort Riccia sorocarpa reveals its thallus is a microbial biodiversity hotspot. We found a significantly richer and more functionally specialized microbiome on the plant compared to the surrounding soil.
Read more:
doi.org/10.1007/s117...
#Microbiome #Liverworts #UWM
Read more:
doi.org/10.1007/s117...
#Microbiome #Liverworts #UWM
Taxonomic and functional differentiation of soil and thallus microbiomes in Riccia sorocarpa - Biologia
Liverworts, as early-diverging land plants, host unique and ecologically important microbiomes, yet remain largely understudied in microbial ecology. In this study, we investigated the taxonomic and functional composition of microbial communities associated with Riccia sorocarpa, focusing on the thallus and adjacent rhizosphere soil. Using nanopore sequencing and metagenomic analysis, we reveal a significantly higher microbial diversity and functional specialization in the thallus microbiome compared to soil. Despite a shared core microbiota, specific bacterial and fungal taxa are selectively enriched in the thallus, likely driven by host-derived factors. Functional profiling highlights an overrepresentation of nitrogen and sulfur cycling, phototrophy, and plant-associated pathways in the thallus, whereas soil communities are dominated by heterotrophic decomposition processes. These findings support the concept of R. sorocarpa as a holobiont and emphasize the ecological and biotechnological potential of liverwort-associated microbiomes. Our results provide new insights into plant-microbe interactions in early land plants and their roles in ecosystem function and resilience.
doi.org
September 26, 2025 at 9:22 PM
Our new study on the liverwort Riccia sorocarpa reveals its thallus is a microbial biodiversity hotspot. We found a significantly richer and more functionally specialized microbiome on the plant compared to the surrounding soil.
Read more:
doi.org/10.1007/s117...
#Microbiome #Liverworts #UWM
Read more:
doi.org/10.1007/s117...
#Microbiome #Liverworts #UWM
We're diving deep into the world of plant biology by studying the liverwort Apopellia endiviifolia.
Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics.
#Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts
Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics.
#Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts
July 29, 2025 at 5:00 AM
We're diving deep into the world of plant biology by studying the liverwort Apopellia endiviifolia.
Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics.
#Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts
Our team will be using the cutting-edge Stereo-seq technology from Stomics to explore its spatial transcriptomics.
#Bryology #Botany #UWM #Stomics #Transcriptomics #Apopellia #liverworts
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....
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU) - BMC Bioinformatics
Background Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal,...
bmcbioinformatics.biomedcentral.com
June 15, 2025 at 7:44 PM
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....
Reposted by Kuba Sawicki
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)
(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
June 4, 2025 at 1:54 PM
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)
(Reads were mapped with minimap2 and identity scores from nanoplot were used for phred score calculations)
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/...
#Botany #UWM
onlinelibrary.wiley.com/doi/10.1111/...
May 29, 2025 at 8:57 AM
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/...
#Botany #UWM
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Kuba Sawicki
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...
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...
Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants
Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha
liverworts and interrogate the mechanisms enabling virulence in non-flowering and
flowering plants. Their resu...
www.cell.com
April 1, 2025 at 7:12 PM
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...
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...
Reposted by Kuba Sawicki
Engineering resistance with help from Liverworts, Mosses and Ferns
@Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...
@Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...
Engineering resistance with help from Liverworts, Mosses and Ferns | John Innes Centre
Plant diversity and synthetic biology offer solutions to the global challenge of crop protection Non-flowering plants such as liverworts, mosses, and ferns belong to divergent lineages with ancient…
www.jic.ac.uk
March 24, 2025 at 11:47 AM
Engineering resistance with help from Liverworts, Mosses and Ferns
@Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...
@Phil_Carella @JohnInnesCentre www.jic.ac.uk/research-imp...
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
#liverworts #epitranscriptomics #Apopellia
March 8, 2025 at 5:58 PM
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
#liverworts #epitranscriptomics #Apopellia
Reposted by Kuba Sawicki
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."
"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."
Elsevier’s stranglehold on academia: How publishers get rich off our data
Academic publishers’ most valuable asset used to be their journals. Now, it’s the data they collect from researchers and then sell. That is extremely concerning, a growing group of Groningen researche...
ukrant.nl
November 25, 2024 at 10:56 PM
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."
"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."
Reposted by Kuba Sawicki
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:
www.nature.com/articles/s41...
Everything on the discoveries in the thread by @chloe-beaulieu.bsky.social
I want to emphasize 5 additional points:
www.nature.com
February 17, 2025 at 10:13 AM
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:
www.nature.com/articles/s41...
Everything on the discoveries in the thread by @chloe-beaulieu.bsky.social
I want to emphasize 5 additional points:
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....
nph.onlinelibrary.wiley.com/doi/full/10....
Evolution of sexual systems and regressive evolution in Riccia
The genus Riccia is the most speciose of the Marchantiopsida, the complex thalloid liverworts. In contrast to the predicted ancestral liverwort and the majority of extant liverworts that are dioicou...
nph.onlinelibrary.wiley.com
February 10, 2025 at 11:31 AM
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....
nph.onlinelibrary.wiley.com/doi/full/10....
Seriously? 1M$ for Q20 short read machine?
January 24, 2025 at 8:28 AM
Seriously? 1M$ for Q20 short read machine?
Reposted by Kuba Sawicki
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...
Plus a whole bunch of updates for dorado polish and the odd misc bug fix.
github.com/nanoporetech...
January 21, 2025 at 3:12 PM
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...
Plus a whole bunch of updates for dorado polish and the odd misc bug fix.
github.com/nanoporetech...
Reposted by Kuba Sawicki
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
January 16, 2025 at 1:30 PM
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
Mk1 family of @nanoporetech.com sequencers
January 21, 2025 at 1:17 PM
Mk1 family of @nanoporetech.com sequencers
New kid on the block 😎
Upgrade of our @nanoporetech.com mk1c
Upgrade of our @nanoporetech.com mk1c
January 20, 2025 at 2:14 PM
New kid on the block 😎
Upgrade of our @nanoporetech.com mk1c
Upgrade of our @nanoporetech.com mk1c
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...
www.nature.com/articles/s41...
Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.) - Scientific Data
Scientific Data - Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)
www.nature.com
January 19, 2025 at 4:06 PM
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...
www.nature.com/articles/s41...
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...
www.nature.com/articles/s41...
Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains, carpathians) - Scientific Report...
Scientific Reports - Reproductive and persistence strategy of the liverwort Arnellia fennica after the last glaciation in the area of disjunction in Central Europe (Polish Tatra Mountains,...
www.nature.com
January 15, 2025 at 2:52 PM
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...
www.nature.com/articles/s41...
Reposted by Kuba Sawicki
📜 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
🧑🔬 @luciaborniego.bsky.social, @msr20.bsky.social, @inneslab.bsky.social, et al.
📔 @pnas.org
🔗 www.pnas.org/doi/10.1073/...
#️⃣ #PlantScience #PlantImmunity #PlantRNAs
Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs | PNAS
Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous
mRNAs in fungal pathogens. Although such host-induced g...
www.pnas.org
January 15, 2025 at 6:32 AM
📜 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
🧑🔬 @luciaborniego.bsky.social, @msr20.bsky.social, @inneslab.bsky.social, et al.
📔 @pnas.org
🔗 www.pnas.org/doi/10.1073/...
#️⃣ #PlantScience #PlantImmunity #PlantRNAs
Adenine DNA methylation associated to transcription is widespread across eukaryotes prelights.biologists.com/highlights/a...
Adenine DNA methylation associated to transcription is widespread across eukaryotes - preLights
Breaking paradigms: Finding 6mA DNA methylation in eukaryotes.
prelights.biologists.com
January 14, 2025 at 3:04 PM
Adenine DNA methylation associated to transcription is widespread across eukaryotes prelights.biologists.com/highlights/a...
Reposted by Kuba Sawicki
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
January 13, 2025 at 5:47 PM
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
Reposted by Kuba Sawicki
Dendrograms in ggplot2 heatmaps 🔥
Check out the great `legendry` package by @teunbrand.bsky.social
github.com/teunbrand/le...
Check out the great `legendry` package by @teunbrand.bsky.social
github.com/teunbrand/le...
January 11, 2025 at 11:49 PM
Dendrograms in ggplot2 heatmaps 🔥
Check out the great `legendry` package by @teunbrand.bsky.social
github.com/teunbrand/le...
Check out the great `legendry` package by @teunbrand.bsky.social
github.com/teunbrand/le...