Zhigui Bao 鲍志贵
@zbao.bsky.social
🌱 PhD student at Weigelworld @plantevolution.bksy.social | Graph pangenome | Population genetics
Reposted by 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.
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.
January 30, 2026 at 12:41 PM
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.
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.
Reposted by Zhigui Bao 鲍志贵
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...
www.nature.com/articles/s41...
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...
www.nature.com
January 30, 2026 at 9:47 AM
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...
www.nature.com/articles/s41...
Reposted by Zhigui Bao 鲍志贵
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!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
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!
Reposted by Zhigui Bao 鲍志贵
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!
github.com/ranwez-searc...
Pretty convenient!
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-...
github.com
January 13, 2026 at 12:42 PM
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!
github.com/ranwez-searc...
Pretty convenient!
Reposted by Zhigui Bao 鲍志贵
Characterising the detectable and invisible fractions of genomic loci under balancing selection https://www.biorxiv.org/content/10.64898/2026.01.13.698512v1
January 13, 2026 at 1:32 PM
Characterising the detectable and invisible fractions of genomic loci under balancing selection https://www.biorxiv.org/content/10.64898/2026.01.13.698512v1
Reposted by Zhigui Bao 鲍志贵
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
www.weizmann.ac.il/plants/voichek
January 11, 2026 at 8:41 PM
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
www.weizmann.ac.il/plants/voichek
Reposted by Zhigui Bao 鲍志贵
Novel genes arise from genomic deletions across the bacterial tree of life www.biorxiv.org/content/10.6... 🧬🖥️🧪 github.com/aryakaul/pre...
January 7, 2026 at 7:00 PM
Novel genes arise from genomic deletions across the bacterial tree of life www.biorxiv.org/content/10.6... 🧬🖥️🧪 github.com/aryakaul/pre...
Reposted by Zhigui Bao 鲍志贵
🧵 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
🎓 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
January 7, 2026 at 11:50 AM
🧵 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
🎓 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
Reposted by Zhigui Bao 鲍志贵
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!
Thanks to those who already shared the link!
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…
www.sciencedirect.com
January 5, 2026 at 9:02 AM
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!
Thanks to those who already shared the link!
Reposted by Zhigui Bao 鲍志贵
The genetics, evolution, and maintenance of a biological rock-paper-scissors game | Science www.science.org/doi/10.1126/...
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...
www.science.org
January 2, 2026 at 2:16 PM
The genetics, evolution, and maintenance of a biological rock-paper-scissors game | Science www.science.org/doi/10.1126/...
Reposted by Zhigui Bao 鲍志贵
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
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
January 2, 2026 at 2:20 PM
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
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
Reposted by Zhigui Bao 鲍志贵
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...
December 26, 2025 at 7:03 PM
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...
Reposted by Zhigui Bao 鲍志贵
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!
Origin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1
December 24, 2025 at 3:59 AM
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!
Reposted by Zhigui Bao 鲍志贵
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!
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!
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 ...
www.biorxiv.org
December 23, 2025 at 7:55 PM
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!
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!
Reposted by Zhigui Bao 鲍志贵
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...
andrewcarroll.github.io/2025/12/23/t...
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....
andrewcarroll.github.io
December 24, 2025 at 1:52 AM
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...
andrewcarroll.github.io/2025/12/23/t...
Reposted by Zhigui Bao 鲍志贵
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
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Zhigui Bao 鲍志贵
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 🧵
Let’s investigate it’s history and outlook 🧵
November 24, 2025 at 10:36 AM
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 🧵
Let’s investigate it’s history and outlook 🧵
Reposted by Zhigui Bao 鲍志贵
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...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
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
docs.google.com
November 24, 2025 at 2:49 PM
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...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Reposted by Zhigui Bao 鲍志贵
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Zhigui Bao 鲍志贵
Revisiting the evidence for long-lived balancing selection in humans. https://www.biorxiv.org/content/10.1101/2025.11.10.687682v1
November 11, 2025 at 1:35 PM
Revisiting the evidence for long-lived balancing selection in humans. https://www.biorxiv.org/content/10.1101/2025.11.10.687682v1
Reposted by Zhigui Bao 鲍志贵
🌱 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
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
Career – Schneeberger Lab
schneebergerlab.org
November 11, 2025 at 9:50 AM
🌱 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
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
Reposted by Zhigui Bao 鲍志贵
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.
November 8, 2025 at 3:42 PM
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.
Reposted by Zhigui Bao 鲍志贵
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...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
October 27, 2025 at 5:53 PM
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...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
Reposted by Zhigui Bao 鲍志贵
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...
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...
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 ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
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...
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...
Reposted by Zhigui Bao 鲍志贵
✨ 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...
www.nature.com/articles/s41...
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-...
www.nature.com
October 16, 2025 at 7:49 AM
✨ 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...
www.nature.com/articles/s41...