Bernard Kim
@bernardkim.bsky.social
Assistant Professor at Princeton EEB. Popgen, evolution, genomics, and large-scale biodiversity datasets. Mostly working on Drosophila for now.
Reposted by Bernard Kim
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
www.biorxiv.org
October 22, 2025 at 5:46 PM
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bernard Kim
Check out our paper in Evolution Letters!
We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇
We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇
How predictably does complex trait adaptation proceed over space and time in wild populations?
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al.
📷: Dr. Rush Dhillon
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al.
📷: Dr. Rush Dhillon
July 31, 2025 at 9:32 PM
Check out our paper in Evolution Letters!
We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇
We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇
Reposted by Bernard Kim
Wish I could be at #Evol2025 this year! I’ll be starting a new lab at NYU this fall, and will be recruiting at all levels. Please spread the word if you know anyone who wants to work on evo. genomics, phylogenies, and comparative development of inverts (like Hawaiian Drosophila!) shchurch.github.io
June 21, 2025 at 9:03 PM
Wish I could be at #Evol2025 this year! I’ll be starting a new lab at NYU this fall, and will be recruiting at all levels. Please spread the word if you know anyone who wants to work on evo. genomics, phylogenies, and comparative development of inverts (like Hawaiian Drosophila!) shchurch.github.io
Reposted by Bernard Kim
I am delighted to be starting as an assistant professor in the Department of Molecular Genetics & Microbiology at the University of Florida in January 2026. The lab is broadly interested in the functional, developmental, and evolutionary genetics of cell types and organs across flies and beyond 🪰🧬
June 18, 2025 at 6:27 PM
I am delighted to be starting as an assistant professor in the Department of Molecular Genetics & Microbiology at the University of Florida in January 2026. The lab is broadly interested in the functional, developmental, and evolutionary genetics of cell types and organs across flies and beyond 🪰🧬
Reposted by Bernard Kim
Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...
Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations
Negative natural selection on deleterious mutations plays a key role in shaping human genetic variation. Understanding the dominance of deleterious mutations is critical as it can fundamentally impact...
www.biorxiv.org
May 8, 2025 at 2:58 PM
Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...
Reposted by Bernard Kim
Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...
Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin
The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the eff...
doi.org
April 25, 2025 at 8:03 PM
Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...
Reposted by Bernard Kim
To my fellow #Drosophila colleagues & friends...
As you know @flybase.bsky.social has been under financial pressure due to #NIH cuts for several years.
With the threats Harvard is currently facing, supporting FlyBase is even more essential. If you have the means, make a tax-deductible donation.
As you know @flybase.bsky.social has been under financial pressure due to #NIH cuts for several years.
With the threats Harvard is currently facing, supporting FlyBase is even more essential. If you have the means, make a tax-deductible donation.
April 17, 2025 at 5:04 PM
To my fellow #Drosophila colleagues & friends...
As you know @flybase.bsky.social has been under financial pressure due to #NIH cuts for several years.
With the threats Harvard is currently facing, supporting FlyBase is even more essential. If you have the means, make a tax-deductible donation.
As you know @flybase.bsky.social has been under financial pressure due to #NIH cuts for several years.
With the threats Harvard is currently facing, supporting FlyBase is even more essential. If you have the means, make a tax-deductible donation.
A lot of folks have asked about gene annotations for the Drosophila genome data. @pankajd.bsky.social and @darrenobbard.bsky.social have something for you!
I know you like #Drosophila and I know you like #Genomes - but do you also like #Genes? Coding DNA annotation of 304 species of Drosophilidae! www.biorxiv.org/content/10.1...
Comparative gene annotation of 304 species of Drosophilidae
www.biorxiv.org
April 16, 2025 at 8:14 PM
A lot of folks have asked about gene annotations for the Drosophila genome data. @pankajd.bsky.social and @darrenobbard.bsky.social have something for you!
Reposted by Bernard Kim
I know you like #Drosophila and I know you like #Genomes - but do you also like #Genes? Coding DNA annotation of 304 species of Drosophilidae! www.biorxiv.org/content/10.1...
Comparative gene annotation of 304 species of Drosophilidae
www.biorxiv.org
April 16, 2025 at 6:21 AM
I know you like #Drosophila and I know you like #Genomes - but do you also like #Genes? Coding DNA annotation of 304 species of Drosophilidae! www.biorxiv.org/content/10.1...
Reposted by Bernard Kim
Preprint alert: FlyCADD! 🧬
Excited to share FlyCADD: impact prediction tool scoring the functional impact of any single nucleotide variant across the entire Drosophila melanogaster genome, to distinguish causal from neutral SNPs
www.biorxiv.org/content/10.1...
Excited to share FlyCADD: impact prediction tool scoring the functional impact of any single nucleotide variant across the entire Drosophila melanogaster genome, to distinguish causal from neutral SNPs
www.biorxiv.org/content/10.1...
Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD
Understanding how genetic variants drive phenotypic differences is a major challenge in molecular biology. Single nucleotide polymorphisms form the vast majority of genetic variation and play critical...
www.biorxiv.org
March 7, 2025 at 2:14 PM
Preprint alert: FlyCADD! 🧬
Excited to share FlyCADD: impact prediction tool scoring the functional impact of any single nucleotide variant across the entire Drosophila melanogaster genome, to distinguish causal from neutral SNPs
www.biorxiv.org/content/10.1...
Excited to share FlyCADD: impact prediction tool scoring the functional impact of any single nucleotide variant across the entire Drosophila melanogaster genome, to distinguish causal from neutral SNPs
www.biorxiv.org/content/10.1...
Please share! In addition an important resource for improving human health, it will grow to be an incredible resource for science. E.g. we envision layering population genomic data across all species and connecting to other insect systems. There are so many cool questions to ask w/this kind of data.
globally, there are ~3500 described mosquito species in the Culicidae family and many of these are important vectors of disease but only a small percentage have genomic resources. we are launching a pilot project to generate high quality reference genomes for 100 important mosquito species [1/3]
February 24, 2025 at 4:30 PM
Please share! In addition an important resource for improving human health, it will grow to be an incredible resource for science. E.g. we envision layering population genomic data across all species and connecting to other insect systems. There are so many cool questions to ask w/this kind of data.
Reposted by Bernard Kim
How is functional variation at large-effect loci maintained in natural populations?
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Dominance reversal maintains large-effect resistance polymorphism in temporally varying environments
A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation1. Theory suggests that dominance reversal, whereby alleles subject to fluctuating selectio...
www.biorxiv.org
January 22, 2025 at 7:44 PM
How is functional variation at large-effect loci maintained in natural populations?
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Reposted by Bernard Kim
Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
Kim Lab at UC Irvine
Visit the post for more.
sskimlab.org
January 20, 2025 at 11:08 PM
Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
With Hannah Gellert, Sam Church, Anton Suvorov,
@petrovadmitri.bsky.social, and others, we use low-input (down to 30ng), single-insect Nanopore sequencing to help do 184 new genomes and address the near absence of genomic data for drosophilid species that cannot be cultured in the lab.
@petrovadmitri.bsky.social, and others, we use low-input (down to 30ng), single-insect Nanopore sequencing to help do 184 new genomes and address the near absence of genomic data for drosophilid species that cannot be cultured in the lab.
Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life https://www.biorxiv.org/content/10.1101/2023.10.02.560517v1
Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life https://www.biorxiv.org/content/10.1101/2023.10.02.560517v1
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, i
www.biorxiv.org
October 4, 2023 at 12:04 AM
With Hannah Gellert, Sam Church, Anton Suvorov,
@petrovadmitri.bsky.social, and others, we use low-input (down to 30ng), single-insect Nanopore sequencing to help do 184 new genomes and address the near absence of genomic data for drosophilid species that cannot be cultured in the lab.
@petrovadmitri.bsky.social, and others, we use low-input (down to 30ng), single-insect Nanopore sequencing to help do 184 new genomes and address the near absence of genomic data for drosophilid species that cannot be cultured in the lab.