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
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...
Reposted by Zhigui Bao 鲍志贵
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...
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 14, 2025 at 12:00 PM
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...
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)
well, well, well 🍿
⬇️
www.biorxiv.org/content/10.1...
Reposted by Zhigui Bao 鲍志贵
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Zhigui Bao 鲍志贵
A deep-time landscape of plant cis-regulatory sequence evolution https://www.biorxiv.org/content/10.1101/2025.09.17.676453v1
September 19, 2025 at 3:03 PM
A deep-time landscape of plant cis-regulatory sequence evolution https://www.biorxiv.org/content/10.1101/2025.09.17.676453v1
Reposted by Zhigui Bao 鲍志贵
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...
doi.org/10.1126/scie...
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...
doi.org
September 18, 2025 at 6:35 PM
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...
doi.org/10.1126/scie...
Reposted by Zhigui Bao 鲍志贵
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
September 15, 2025 at 8:44 AM
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
Reposted by Zhigui Bao 鲍志贵
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
), we find the opposite: animals exchange genes more, and for longer, than plants
September 12, 2025 at 7:55 AM
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
), we find the opposite: animals exchange genes more, and for longer, than plants
Reposted by Zhigui Bao 鲍志贵
"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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 17, 2025 at 10:53 PM
"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...
www.biorxiv.org/content/10.1...
Reposted by Zhigui Bao 鲍志贵
Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1
August 15, 2025 at 3:48 AM
Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes https://www.biorxiv.org/content/10.1101/2025.08.14.670405v1
Reposted by Zhigui Bao 鲍志贵
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.
Illustration: Genetically diverse Arabidopsis grown in the lab | Closely related wild Arabidopsis during the natural growing season | Diversity of Arabidopsis habitats.
August 14, 2025 at 3:44 PM
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.
Illustration: Genetically diverse Arabidopsis grown in the lab | Closely related wild Arabidopsis during the natural growing season | Diversity of Arabidopsis habitats.
Reposted by Zhigui Bao 鲍志贵
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
"Pangenomic context reveals the extent of intraspecific plant NLR evolution"
www.cell.com/cell-host-mi...
#plantscience #plantimmunity #pangenomes #science #nlr
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...
www.cell.com
August 14, 2025 at 5:55 AM
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
"Pangenomic context reveals the extent of intraspecific plant NLR evolution"
www.cell.com/cell-host-mi...
#plantscience #plantimmunity #pangenomes #science #nlr
So cool!
To promote the collection, I’ve launched a designer clothing line where synthetic biology meets aesthetics.
I will give out 100 free limited edition shirts to the first who retweet and order with their handle in the name! Available here → nickdesnoyer.com 🧵(6/7)
I will give out 100 free limited edition shirts to the first who retweet and order with their handle in the name! Available here → nickdesnoyer.com 🧵(6/7)
August 11, 2025 at 7:00 PM
So cool!
Reposted by Zhigui Bao 鲍志贵
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
August 5, 2025 at 6:48 PM
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
Reposted by Zhigui Bao 鲍志贵
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
July 18, 2025 at 5:05 PM
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
Reposted by Zhigui Bao 鲍志贵
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...
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...
July 16, 2025 at 5:51 PM
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...
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...
Reposted by Zhigui Bao 鲍志贵
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
July 17, 2025 at 7:53 AM
Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!
Reposted by Zhigui Bao 鲍志贵
Accurate diagram 😂
We finished this edition with a delightful keynote by Jean Monlong who guided us through his journey about finding SVs in pangenomes #JOBIM2025 👏🏻
July 11, 2025 at 2:03 PM
Accurate diagram 😂
Reposted by Zhigui Bao 鲍志贵
Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718
July 8, 2025 at 2:14 AM
Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718
Reposted by Zhigui Bao 鲍志贵
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
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
July 7, 2025 at 8:31 AM
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
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
Reposted by Zhigui Bao 鲍志贵
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...
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...
www.biorxiv.org
July 2, 2025 at 11:46 PM
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...