Zhigui Bao 鲍志贵
@zbao.bsky.social
📤 186
📥 175
📝 49
🌱 PhD student at Weigelworld
@plantevolution.bksy.social
| Graph pangenome | Population genetics
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Zhigui Bao 鲍志贵
Adam Phillippy
about 14 hours ago
If you’ve heard me talk in the past ~5 years, you will know I have developed an obsession with acrocentric chromosomes. This is all of that, condensed into one paper. I will do a full thread in the new year, but for those that want something to read over the holidays, have at it. Such a cool story!
add a skeleton here at some point
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Zhigui Bao 鲍志贵
Antonio Scialdone
about 22 hours ago
Our new preprint is out:
www.biorxiv.org/content/10.6...
We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!
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Hidden sampling biases inflate performance in gene regulatory network inference
Accurate reconstruction of gene regulatory networks (GRNs) from single-cell transcriptomic data remains a major methodological challenge. Recent machine learning approaches, particularly graph neural ...
https://www.biorxiv.org/content/10.64898/2025.12.19.695616v1
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Zhigui Bao 鲍志贵
Andrew Carroll
about 16 hours ago
I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.
andrewcarroll.github.io/2025/12/23/t...
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The Virtual Cell Will Be More Like Gwas Than Alphafold
There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....
https://andrewcarroll.github.io/2025/12/23/the-virtual-cell-will-be-more-like-GWAS-than-AlphaFold.html
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Zhigui Bao 鲍志贵
Aaron Quinlan (he/him)
23 days ago
We are thrilled to announce the first official release (v0.1.8) of
#𝗯𝗲𝗱𝗱𝗲𝗿
, the successor to one of our flagship tool,
#𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀
! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n
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Intro to Bedder – The Quinlan Lab
http://quinlanlab.org/blogposts/bedder_intro.html
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Zhigui Bao 鲍志贵
Nick Desnoyer
about 1 month ago
With the 50-year rise of Arabidopsis as the most studied plant, is it time for its downfall? Let’s investigate it’s history and outlook 🧵
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Zhigui Bao 鲍志贵
PlantEvolution 🌱🌾
about 1 month ago
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the
#Arabidopsis
#1001GenomesPlus
project. We have now a curated collection of over 500 long read genomes. Please help us by filling out this questionnaire:
docs.google.com/forms/d/e/1F...
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Next generation of 1001 Genomes Plus browser and data download
Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes
https://docs.google.com/forms/d/e/1FAIpQLScPNWRqlhU5N8KejJgemzRQaYAmYT72pv_joINgejwqahSF3g/viewform
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Zhigui Bao 鲍志贵
Sasha Gusev
about 1 month ago
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
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The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
https://theinfinitesimal.substack.com/p/the-missing-heritability-question?r=43f9ax&utm_campaign=post&utm_medium=web&triedRedirect=true
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Zhigui Bao 鲍志贵
bioRxiv Evolutionary Biology
about 1 month ago
Revisiting the evidence for long-lived balancing selection in humans.
https://www.biorxiv.org/content/10.1101/2025.11.10.687682v1
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Zhigui Bao 鲍志贵
Schneeberger Lab
about 1 month ago
🌱 Postdoc position in Plant Genomics/Bioinformatics! Love genome plasticity, computational methods, and solving big questions in plant biology? Join our newly established Institute for Crop Biology at HHU Düsseldorf. More info on
schneebergerlab.org/career/
Apply by Nov. 30 | 3-year position
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Career – Schneeberger Lab
https://schneebergerlab.org/career/
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Zhigui Bao 鲍志贵
Angela Hancock
about 2 months ago
I recently moved my lab to Purdue University and am looking for graduate students. We are working at the interface of population genomics, quantitative genetics and functional genomics to understand how plants adapt to extreme environments. Reach out if you would like to discuss potential projects.
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Zhigui Bao 鲍志贵
PlantEvolution 🌱🌾
about 2 months ago
1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by
@zbao.bsky.social
! Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes
#plantscience
#genomegraphs
www.cambridge.org/core/journal...
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Zhigui Bao 鲍志贵
Sternberg Lab
2 months ago
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
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Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
https://www.biorxiv.org/content/10.1101/2025.10.16.682844v1
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Zhigui Bao 鲍志贵
Joseph Schacherer
2 months ago
✨ Latest exciting story of the group in
@nature.com
. Here, we go beyond SNPs and built a species-wide atlas of genetic variants in yeast. With >1,000 near T2T genomes, we show how large genomic variations affect trait diversity.
www.nature.com/articles/s41...
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From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes - Nature
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-...
https://www.nature.com/articles/s41586-025-09637-0
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Zhigui Bao 鲍志贵
Alexis Verger 🧬🧫🧪
2 months ago
Remember this paper "Low overlap of transcription factor DNA binding and regulatory targets" ? (
www.nature.com/articles/s41...
) well, well, well 🍿 ⬇️
www.biorxiv.org/content/10.1...
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On the overlap of transcription factor binding and regulatory targets: functional and regulatory coherence of top-bound targets is masked by weakly bound ones
A recent study that systematically mapped genomic bindings and regulatory effects of transcription factors (TFs) reported a surprisingly low overlap between TF binding and regulatory targets in Saccha...
https://www.biorxiv.org/content/10.1101/2025.10.12.681120v1
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Zhigui Bao 鲍志贵
Yun S. Song
3 months ago
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
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Zhigui Bao 鲍志贵
bioRxiv Plant Bio
3 months ago
A deep-time landscape of plant cis-regulatory sequence evolution
https://www.biorxiv.org/content/10.1101/2025.09.17.676453v1
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Zhigui Bao 鲍志贵
Pierre Baduel
3 months ago
Happy to share the results of a long-haul post-doc project, now online
@science.org
, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below!
doi.org/10.1126/scie...
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Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
https://doi.org/10.1126/science.ady3475
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Zhigui Bao 鲍志贵
PLOS Biology
3 months ago
The
#Drosophila
Dscam1 gene generates 10000s of isoforms, but only a small fraction supports neuronal functions. This study shows that
#fitness
&
#immunity
are the likely primary evolutionary drivers of Dscam1 isoform diversity in
#arthropods
@plosbiology.org
🧪
plos.io/4gp8cWd
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Zhigui Bao 鲍志贵
Camille Roux
3 months ago
Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (
www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants
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Zamin Iqbal
4 months ago
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...
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Protein structure alignment significance is often exaggerated
Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...
https://www.biorxiv.org/content/10.1101/2025.07.17.665375v1
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Zhigui Bao 鲍志贵
bioRxiv Bioinfo
4 months ago
Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes
https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1
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Zhigui Bao 鲍志贵
PlantEvolution 🌱🌾
4 months ago
2/2 With @derekseveri.bsky.social, Joy Bergelson, Fabrice Roux and Talia Karasov. Illustration: Genetically diverse Arabidopsis grown in the lab | Closely related wild Arabidopsis during the natural growing season | Diversity of Arabidopsis habitats.
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Zhigui Bao 鲍志贵
K.D. Murray
4 months ago
Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution"
www.cell.com/cell-host-mi...
#plantscience
#plantimmunity
#pangenomes
#science
#nlr
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Pangenomic context reveals the extent of intraspecific plant NLR evolution
Individual- and population-level diversity is required for pathogen defense by nucleotide-binding site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent A. thaliana gen...
https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(25)00283-5
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So cool!
add a skeleton here at some point
4 months ago
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Zhigui Bao 鲍志贵
Ryan Gutenkunst
5 months ago
If you're new to demographic history inference from population genomics, try this webapp I created to illustrate how dadi fits bottleneck models to site frequency spectra:
ryangutenkunst-dadi-two-epoch.hf.space
. It even outputs files for submitting to the GHIST competition!
ghi.st
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Zhigui Bao 鲍志贵
bioRxiv Plant Bio
5 months ago
Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana
https://www.biorxiv.org/content/10.1101/2025.07.14.664700v1
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Zhigui Bao 鲍志贵
Laurie Belcher
5 months ago
OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10)
github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...
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Zhigui Bao 鲍志贵
Erik Garrison
5 months ago
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
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Zhigui Bao 鲍志贵
Adam Phillippy
6 months ago
Accurate diagram 😂
add a skeleton here at some point
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Zhigui Bao 鲍志贵
Heng Li
6 months ago
Preprint on "Finding easy regions for short-read variant calling from pangenome data":
arxiv.org/abs/2507.03718
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Zhigui Bao 鲍志贵
Ulrich Lutz
6 months ago
New paper out! 🎉 With an innovative approach of CRISPRing a gene mutation on many backgrounds, we provide a proof of concept for how “pan-genetic” analysis can reveal the true extent of genetic networks in a species. Thanks @plantevolution.bsky.social-lab! Open-access:
tinyurl.com/3aw7t6ff
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Zhigui Bao 鲍志贵
David A Knowles
6 months ago
New work from the lab trying to wrap our heads around the massive complexity of the human transcriptome revealed by long-read RNA-seq! Fun collab with Gloria Sheynkman.
www.biorxiv.org/content/10.1...
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Perplexity as a Metric for Isoform Diversity in the Human Transcriptome
Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologic...
https://www.biorxiv.org/content/10.1101/2025.07.02.662769v1
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Zhigui Bao 鲍志贵
North American Arabidopsis Steering Committee
6 months ago
Detlef Weigel- Max Planck Inst- Tubingen- honored for his lifetime of excellence in research, mentorship, and support of the Arabidopsis community
#ICAR2025
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Zhigui Bao 鲍志贵
Heng Li
6 months ago
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
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Zhigui Bao 鲍志贵
Andrew Hipp
6 months ago
Long-term flowering-time data on Japanese mountain cherry (recorded since the 9th century!) shows a shift in full-flowering date beginning in the late 19th century. Fascinating new
@newphyt.bsky.social
paper by
@jgpausas.bsky.social
onlinelibrary.wiley.com/doi/abs/10.1...
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Zhigui Bao 鲍志贵
Science Magazine
6 months ago
As the world warms, plants in natural ecosystems and agricultural settings find ways to respond to the heat. In a new special issue of Science, researchers examine how heat affects plants at multiple scales, from the molecular level to the biosphere.
scim.ag/44cSw3Z
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Zhigui Bao 鲍志贵
Vaughn Cooper
7 months ago
Sharing the most significant work from my group, led by the
@evolvingstem.bsky.social
team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵
www.biorxiv.org/content/10.1...
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Student-led experimental evolution reveals novel biofilm regulatory networks underlying adaptations to multiple niches
We established a research-education partnership known as EvolvingSTEM that provides secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution....
https://www.biorxiv.org/content/10.1101/2025.06.06.658356v1
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Lisa Smith
7 months ago
With the publication of a new preprint (
www.biorxiv.org/content/10.1...
) with collaborators
@labschneeberger.bsky.social
@plantevolution.bsky.social
and
@jurriaanton.bsky.social
, I feel it is timely to talk about what will probably be the most successful 'failed' experiment of my career.
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The mutational dynamics of the Arabidopsis centromeres
Centromeres are specialized chromosome regions essential for sister chromatid cohesion and spindle attachment during mitosis. Many centromeres comprise highly variable, megabase-scale satellite DNA ar...
https://www.biorxiv.org/content/10.1101/2025.06.02.657473v1
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Zhigui Bao 鲍志贵
bioRxiv Evolutionary Biology
7 months ago
Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana
https://www.biorxiv.org/content/10.1101/2025.05.28.654549v1
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Zhigui Bao 鲍志贵
Zeqian Li
7 months ago
I started tgv to learn Rust and building it has been unbelievably fun! If you wanna pick up a super fast and fun programming language, tgv is open for contribution! There aren't many bioinformatics tools built entirely by the community. If tgv can become one, I'll be so psyched
add a skeleton here at some point
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Zhigui Bao 鲍志贵
Charlie Pugh
7 months ago
New preprint in collaboration with
@paulinanunezv.bsky.social
supervised by
@jonnyfrazer.bsky.social
and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n
www.biorxiv.org/content/10.1...
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From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...
https://www.biorxiv.org/content/10.1101/2025.05.20.655154v1
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Zhigui Bao 鲍志贵
Roeder Lab
7 months ago
Check out the beautiful cover to our focus issue on Translational research from Arabidopsis to crop plants and beyond. More articles coming shortly. Congrats Patrice Salome and
@jotlovell.bsky.social
.
@theplantcell.bsky.social
academic.oup.com/plcell/issue...
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Zhigui Bao 鲍志贵
Molecular Biology and Evolution
8 months ago
Ancestral sequence reconstruction often assumes unrealistic homogeneous substitution models; however
@rmuniztrejo.bsky.social
et al. find that reconstruction accuracy is determined by phylogenetic signal, not model choice. 🔗
doi.org/10.1093/molb...
#evobio
#molbio
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Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity
Abstract. Ancestral sequence reconstruction is typically performed using homogeneous evolutionary models, which assume that the same substitution propensit
https://doi.org/10.1093/molbev/msaf084
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Zhigui Bao 鲍志贵
Dmitri Petrov
8 months ago
A ridiculous amount of very careful work by
@jahemker.bsky.social
and coauthors gave a clear answer - one needs ultra-long and not just long reads to call SVs correctly in Drosophila. Now we are ready to quantify evolutionary impact of Drosophila SVs. Let us know what you think!
add a skeleton here at some point
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Zhigui Bao 鲍志贵
Francis M. Martin
8 months ago
Conventional and organic farms with more intensive management have lower soil functionality | Science
www.science.org/doi/10.1126/...
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Conventional and organic farms with more intensive management have lower soil functionality
Organic farming is often considered to be more sustainable than conventional farming. However, both farming systems comprise highly variable management practices. In this study, we show that in organi...
https://www.science.org/doi/10.1126/science.adr0211?utm_source=sfmc&utm_medium=email&utm_content=alert&utm_campaign=SCIeToc&et_rid=495898616&et_cid=5597924
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Zhigui Bao 鲍志贵
Dan Kliebenstein
8 months ago
Have you ever wondered how a specialized metabolite enzyme/gene under fluctuating selection goes through speciation? Well the answer is it gets lost a lot. And by a lot we mean a lot. >25 gene copies were empirically tested using a phylo-functional approach.
www.biorxiv.org/content/10.1...
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Convergence and constraint in glucosinolate evolution across the Brassicaceae
Diversity in plant specialized metabolites plays critical roles in plant-environment interactions. In longer evolutionary scales, e.g. between families or orders, this diversity arises from whole-geno...
https://www.biorxiv.org/content/10.1101/2025.04.23.650103v1
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Zhigui Bao 鲍志贵
Heng Li
8 months ago
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng:
www.biorxiv.org/content/10.1...
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Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1
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8 months ago
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Karel Břinda
9 months ago
A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in
@naturemethods.bsky.social
answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/
@baym.lol
,
@zaminiqbal.bsky.social
et al. 🧵1/
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Shujun Ou
9 months ago
Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n
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