Rory Kirchner
@roryk.bsky.social
Computational Biologist at Ginkgo Bioworks
Reposted by Rory Kirchner
How population stratification makes environments look like genes. A short 🧵:
January 20, 2025 at 7:09 PM
How population stratification makes environments look like genes. A short 🧵:
Reposted by Rory Kirchner
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:54 AM
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
Reposted by Rory Kirchner
We also revealed that the use of MALAT1 expression as a surrogate for nuclear content is a promising solution, particularly when raw intronic data is unavailable.
5/8
5/8
December 3, 2024 at 8:38 AM
We also revealed that the use of MALAT1 expression as a surrogate for nuclear content is a promising solution, particularly when raw intronic data is unavailable.
5/8
5/8
Reposted by Rory Kirchner
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
So glad a large portion of my Twitter science crew has relocated to Bluesky.
November 22, 2024 at 2:33 PM
So glad a large portion of my Twitter science crew has relocated to Bluesky.
Reposted by Rory Kirchner
You forgot to add Nature/Science/Cell before that. Without that prefix the journal is worthless.
Journal of Irreproducible Results - 👎🤮
Nature Journal of Irreproducible Results - 👍🤩
Journal of Irreproducible Results - 👎🤮
Nature Journal of Irreproducible Results - 👍🤩
November 22, 2024 at 10:01 AM
You forgot to add Nature/Science/Cell before that. Without that prefix the journal is worthless.
Journal of Irreproducible Results - 👎🤮
Nature Journal of Irreproducible Results - 👍🤩
Journal of Irreproducible Results - 👎🤮
Nature Journal of Irreproducible Results - 👍🤩
Reposted by Rory Kirchner
now I've heard there was a secret
beastie boys: CHORD
that david played and it pleased the
beastie boys: LORD
but you don't really care for music
beastie boys: DO YA
beastie boys: CHORD
that david played and it pleased the
beastie boys: LORD
but you don't really care for music
beastie boys: DO YA
June 3, 2023 at 10:59 PM
now I've heard there was a secret
beastie boys: CHORD
that david played and it pleased the
beastie boys: LORD
but you don't really care for music
beastie boys: DO YA
beastie boys: CHORD
that david played and it pleased the
beastie boys: LORD
but you don't really care for music
beastie boys: DO YA