Bernard Kim
@bernardkim.bsky.social
Assistant Professor at Princeton EEB. Popgen, evolution, genomics, and large-scale biodiversity datasets. Mostly working on Drosophila for now.
Huge congrats and see you soon on the East Coast!
June 22, 2025 at 6:18 PM
Huge congrats and see you soon on the East Coast!
Cool paper, congrats Jun!
May 8, 2025 at 4:31 PM
Cool paper, congrats Jun!
Note that this approach uses public data and comparative annotation, but no new transcriptome data. New RNA-seq data for select key taxa is in the works but will take some time to complete.
April 16, 2025 at 8:19 PM
Note that this approach uses public data and comparative annotation, but no new transcriptome data. New RNA-seq data for select key taxa is in the works but will take some time to complete.
Ha, thank you! You might also be interested to know that these patterns are correlated with function too.
October 5, 2023 at 4:33 AM
Ha, thank you! You might also be interested to know that these patterns are correlated with function too.
Much credit and thanks to all of the wonderful co-authors who make this kind of work possible!
October 4, 2023 at 12:09 AM
Much credit and thanks to all of the wonderful co-authors who make this kind of work possible!
We’re particularly excited this as a framework for connecting micro- to macro-evolution in this group. One early look at a fascinating result: a 2400 residue protein where polymorphism across ~30spp matches substitutions (neutral evolution) across ~30 million years. More soon!
October 4, 2023 at 12:08 AM
We’re particularly excited this as a framework for connecting micro- to macro-evolution in this group. One early look at a fascinating result: a 2400 residue protein where polymorphism across ~30spp matches substitutions (neutral evolution) across ~30 million years. More soon!
We have more coming in the near future, including a comprehensive Drosophilidae Tree of Life integrating whole-genome data (pictured phylogeny) with classic markers (not shown), RNA-seq for annotation, and population genomic data for >100 species.
October 4, 2023 at 12:08 AM
We have more coming in the near future, including a comprehensive Drosophilidae Tree of Life integrating whole-genome data (pictured phylogeny) with classic markers (not shown), RNA-seq for annotation, and population genomic data for >100 species.
This effort is being managed as an open science, community resource. Data are on NCBI, containerized+Snakemake pipelines on GitHub, public protocols, and a 298-way Cactus alignment is available for download. Please see the preprint for more details on accessing these resources.
October 4, 2023 at 12:08 AM
This effort is being managed as an open science, community resource. Data are on NCBI, containerized+Snakemake pipelines on GitHub, public protocols, and a 298-way Cactus alignment is available for download. Please see the preprint for more details on accessing these resources.
We are continuing our sequencing with the goal of hitting 1,000 drosophilid genomes by the end of next year. Please reach out if you are interested in collaborating on genomes: no cost to you and the only stipulation is open data.
October 4, 2023 at 12:08 AM
We are continuing our sequencing with the goal of hitting 1,000 drosophilid genomes by the end of next year. Please reach out if you are interested in collaborating on genomes: no cost to you and the only stipulation is open data.
We are ironing out some issues with shorter (~1kbp N50) ONT sequencing runs that might be related to the recent light issue.
October 4, 2023 at 12:07 AM
We are ironing out some issues with shorter (~1kbp N50) ONT sequencing runs that might be related to the recent light issue.
This approach also worked surprisingly well for ethanol-preserved specimens, opening up older collections to genomic study and helping us add many esoteric taxa to the tree.
October 4, 2023 at 12:07 AM
This approach also worked surprisingly well for ethanol-preserved specimens, opening up older collections to genomic study and helping us add many esoteric taxa to the tree.
We’ve done lots of fresh collections of wild flies over the last couple years: across the Hawaiian Islands, the Western US (CA, OR, WA, MT, ID, CO), the Midwest (MI, OH), Europe (UK) and were able to assemble single-fly genomes for every species we collected.
October 4, 2023 at 12:07 AM
We’ve done lots of fresh collections of wild flies over the last couple years: across the Hawaiian Islands, the Western US (CA, OR, WA, MT, ID, CO), the Midwest (MI, OH), Europe (UK) and were able to assemble single-fly genomes for every species we collected.