Zhigui Bao 鲍志贵

This article is now published! academic.oup.com/nargab/artic...
We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

Wow! This is consistent with our observation, helixer learn really well in the reference annotation, but when genes are not present in the reference, the annotation will be harder. As it does quite a good job for core genes. Another tool ANNEVO also have similiar small introns/exons issue

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

GitHub - ranwez-search/SeqTUI: A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all ... A fast terminal-based viewer and command-line toolkit for molecular sequences (DNA, AA). View, translate, convert (to FASTA), and combine sequences aligned or not — all from the terminal. - ranwez-...

Just sharing new tool written by Vincent Ranwez to view and manipulate sequences and alignments directly in your terminal
github.com/ranwez-searc...
Pretty convenient!

Characterising the detectable and invisible fractions of genomic loci under balancing selection https://www.biorxiv.org/content/10.64898/2026.01.13.698512v1

The (Yoav) Voichek lab has opened its gates at the Weizmann Institute, and is actively recruiting students and researchers at all levels - come explore gene regulation and computational genomics in a fun, friendly sprouting lab 🤗🥼⚗️🧪
www.weizmann.ac.il/plants/voichek

Novel genes arise from genomic deletions across the bacterial tree of life www.biorxiv.org/content/10.6... 🧬🖥️🧪 github.com/aryakaul/pre...

🧵 Just out in Cell after more than 10 years in the making!

🎓 www.cell.com/cell/fulltex...

Plants and animals evolve radically different body plans.

Do they also operate under fundamentally different molecular evolutionary constraints during organ formation?

@cellpress.bsky.social

Plants tend to lose micro-synteny even at the family level, while animals share much higher percentage of synteny even between orders (www.pnas.org/doi/10.1073/...). They use similar methods to analyze the NLR in angiosperms; it seems the MHC-like locus didn't exist academic.oup.com/mbe/article/...

Did you seen the improvements of splice site also benefit the pangene identification?

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti...
Thanks to those who already shared the link!

The genetics, evolution, and maintenance of a biological rock-paper-scissors game Side-blotched lizards (Uta stansburiana) play a biological rock-paper-scissors game in which three differently colored male morphs utilize alternative mating strategies. We identified the genetic basi...

The genetics, evolution, and maintenance of a biological rock-paper-scissors game | Science www.science.org/doi/10.1126/...

Genome editing in brown algae! 🧬🪸🌿 Now out in Cell Reports Methods!

Excited to share this highly efficient, transgene-free CRISPR–Cas genome editing protocol for brown algae, requiring no cloning and no specialized equipment.

doi.org/10.1016/j.cr...

#CRISPR #BrownAlgae
@mpi-bio-fml.bsky.social

Pandagma: A tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications academic.oup.com/bioinformati... 🧬🖥️ github.com/legumeinfo/p...

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!

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 ...

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!

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...

T2T2T genome

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

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 🧵

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

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...

The missing heritability question is now (mostly) answered Not with a bang but with a whimper

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

Revisiting the evidence for long-lived balancing selection in humans. https://www.biorxiv.org/content/10.1101/2025.11.10.687682v1

🌱 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

PhD advert

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.

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...

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 ...

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...

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-...

✨ 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...

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...

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...