Chongyuan Luo
@chongyuanluo.bsky.social
We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
October 15, 2025 at 4:32 PM
We like to introduce map3C, developed by Joseph Galasso, that drastically improves the mapping and contact calling performance of snm3C-seq and now enables accurate 3D genome modeling. map3C was developed in collaboration with
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Jason Ernst and Frank Alber. www.biorxiv.org/content/10.1...
Congrats to Terence Li on publishing his reviewed preprint in @elife.bsky.social "The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments" elifesciences.org/reviewed-pre...
The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments
Altmetric provides a collated score for online attention across various platforms and media.See more details
elifesciences.org
July 10, 2025 at 3:50 PM
Congrats to Terence Li on publishing his reviewed preprint in @elife.bsky.social "The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments" elifesciences.org/reviewed-pre...
Preprint alert: single-cell methylation signature of autism in collaboration with Dan Geschwind. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by @GeschwindLab Postdoc Katie Eyring and grad student Cuining Liu.
A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures https://www.biorxiv.org/content/10.1101/2025.06.17.660162v1
June 23, 2025 at 3:06 PM
Preprint alert: single-cell methylation signature of autism in collaboration with Dan Geschwind. Autism-mC signal is enriched in promoters and cell-type enhancers but uncorrelated with gene expression. Led by @GeschwindLab Postdoc Katie Eyring and grad student Cuining Liu.
As many of us in genomics know, NIH's bread & butter mechanism historically struggles to fund data generation due to the "hypothesis-driven" dogma. Instead of sporadically using the RFA to fund data generation, this is the time to have a core structure
March 4, 2025 at 7:25 PM
As many of us in genomics know, NIH's bread & butter mechanism historically struggles to fund data generation due to the "hypothesis-driven" dogma. Instead of sporadically using the RFA to fund data generation, this is the time to have a core structure
assuming NIH survives the current trauma, it needs to develop innovative structures to fund SO MUCH data generation to support the AI-powered discoveries unless the plan is to cede the job to @cziscience or start-ups like vevo_ai
March 4, 2025 at 7:25 PM
assuming NIH survives the current trauma, it needs to develop innovative structures to fund SO MUCH data generation to support the AI-powered discoveries unless the plan is to cede the job to @cziscience or start-ups like vevo_ai
I don't know how the dogma that "research should be hypothesis-driven" can still operate in the era of rapid data interpretation by AI models. In the past 25 yrs, genomics field has advocated for systematic data generation the debate may be now settled by the data-hungry models
March 4, 2025 at 6:01 PM
I don't know how the dogma that "research should be hypothesis-driven" can still operate in the era of rapid data interpretation by AI models. In the past 25 yrs, genomics field has advocated for systematic data generation the debate may be now settled by the data-hungry models
Illumina looks pretty good this yr with constellation, single cell, spatial, and five base after I don’t even know how many yrs of looking boring. #AGBTGM
February 24, 2025 at 5:56 PM
Illumina looks pretty good this yr with constellation, single cell, spatial, and five base after I don’t even know how many yrs of looking boring. #AGBTGM
Does ambient RNA/DNA confound the genotype-based demultiplex of 10x Multi-ome data? Terence Li, a bioinfo grad student in Noah Zaitlen lab and my lab investigated precisely this question and provided practical recommendations. www.biorxiv.org/content/10.1...
The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments
Sample multiplexing has become an increasingly common design choice in droplet-based single-nucleus multi-omic sequencing experiments to reduce costs and remove technical variation. Genotype-based dem...
www.biorxiv.org
February 10, 2025 at 9:36 PM
Does ambient RNA/DNA confound the genotype-based demultiplex of 10x Multi-ome data? Terence Li, a bioinfo grad student in Noah Zaitlen lab and my lab investigated precisely this question and provided practical recommendations. www.biorxiv.org/content/10.1...
Reposted by Chongyuan Luo
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
February 8, 2025 at 9:21 PM
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
Reposted by Chongyuan Luo
1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders.
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders
High-throughput experimental validation of genetic variants linked to eight psychiatric
disorders reveals the regulatory mechanisms underlying variants with pleiotropic and
disorder-specific effects.
www.cell.com
January 27, 2025 at 7:02 PM
1/ I am beyond thrilled to share our new paper in @CellCellPress! We explored the regulatory principles underlying pleiotropy in psychiatric disorders.
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
Paperpile @paperpile.com works best if all references are imported using PMID. Letting Paperpile search from random Web sources causes inconsistency in formatting and missing PMCID.
January 24, 2025 at 5:03 PM
Paperpile @paperpile.com works best if all references are imported using PMID. Letting Paperpile search from random Web sources causes inconsistency in formatting and missing PMCID.
Paperpile @paperpile.com can you remove URLs from the "National Library of Medicine (grant proposals with PMCID/PMID)" format? This format is fantastic but NIH does not allow URLs in grant proposals
January 22, 2025 at 5:46 PM
Paperpile @paperpile.com can you remove URLs from the "National Library of Medicine (grant proposals with PMCID/PMID)" format? This format is fantastic but NIH does not allow URLs in grant proposals
~20 yrs ago I chose bio major because bio requires the least amount of math but look where we are now
Whoa! When a large language of life model generates a protein equivalent to ~500 million years of evolution.
@science.org
science.org/doi/10.1126/...
@science.org
science.org/doi/10.1126/...
Simulating 500 million years of evolution with a language model
More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained at scale on evolutionary data can gen...
science.org
January 16, 2025 at 11:14 PM
~20 yrs ago I chose bio major because bio requires the least amount of math but look where we are now
Reposted by Chongyuan Luo
our newest preprint! Led by Zoe Grant in my lab and Shuzen Kuang in Katie Pollard's lab here at Gladstone. "Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor" 1/n www.biorxiv.org/content/10.1...
January 13, 2025 at 5:07 PM
our newest preprint! Led by Zoe Grant in my lab and Shuzen Kuang in Katie Pollard's lab here at Gladstone. "Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor" 1/n www.biorxiv.org/content/10.1...
Reposted by Chongyuan Luo
UCLA QCBIO is looking for its next director! Please consider applying! recruit.apo.ucla.edu/JPF10007
Director, Institute for Quantitative and Computational Biosciences
University of California, Los Angeles is hiring. Apply now!
recruit.apo.ucla.edu
January 6, 2025 at 11:35 PM
UCLA QCBIO is looking for its next director! Please consider applying! recruit.apo.ucla.edu/JPF10007
Not publishing that last dull paper from the old lab is always a mistake because track records belong to you, not just to the lab, and you don't know how well the new thing/place will work out and maybe that dull paper will get you the next big job, you never know.
January 6, 2025 at 11:23 PM
Not publishing that last dull paper from the old lab is always a mistake because track records belong to you, not just to the lab, and you don't know how well the new thing/place will work out and maybe that dull paper will get you the next big job, you never know.
I am lost in why NIH issues all these NOSIs with no dedicated review panel and no allocated budget. Giving the impression of top-down planning (which many people dislike) but giving no priority to people who respond seems to defeat a whole lot of purposes all at the same time
January 6, 2025 at 5:20 PM
I am lost in why NIH issues all these NOSIs with no dedicated review panel and no allocated budget. Giving the impression of top-down planning (which many people dislike) but giving no priority to people who respond seems to defeat a whole lot of purposes all at the same time
the late 2020 H1B rule change raised minimal salary to $85k and that applied to cap-exempt academic H1B. That was about to eliminate >5 yr positions (beyond J1) for many international postdocs. If comes back, an $100k line would be nothing for tech but a big problem for labs
December 31, 2024 at 6:04 PM
the late 2020 H1B rule change raised minimal salary to $85k and that applied to cap-exempt academic H1B. That was about to eliminate >5 yr positions (beyond J1) for many international postdocs. If comes back, an $100k line would be nothing for tech but a big problem for labs
If you wonder why people have jumped into scRNA-seq and CRISPR in an almost uninspiring way, a simple explanation is that the shortage of methods for measuring and modifying remains the bottleneck of biology and will remain so for a long time.
have ppl found any funders that support toolmaking? I want to keep making tools for people, but there is a seemingly irresistible force pushing us towards hypothesis-driven research. In my experience, funders don't want to hear about tech dev. Any insights? for both neuro & climate would be great tx
December 23, 2024 at 8:09 PM
If you wonder why people have jumped into scRNA-seq and CRISPR in an almost uninspiring way, a simple explanation is that the shortage of methods for measuring and modifying remains the bottleneck of biology and will remain so for a long time.
However, I did notice the possibility that some grad school applicants abuse bioRxiv by posting manuscripts that practically can't get through any serious peer review.
December 22, 2024 at 7:08 PM
However, I did notice the possibility that some grad school applicants abuse bioRxiv by posting manuscripts that practically can't get through any serious peer review.
bioRxiv has transformed the publication of biological research. All these tweaking of open access policy, not so much.
December 22, 2024 at 7:04 PM
bioRxiv has transformed the publication of biological research. All these tweaking of open access policy, not so much.
The impact of luck is one of my favorite topics when I talk about scientific careers with family & friends. Basically, I think luck is a lot more important than my effort.
December 9, 2024 at 6:58 PM
The impact of luck is one of my favorite topics when I talk about scientific careers with family & friends. Basically, I think luck is a lot more important than my effort.
Hiring more faculty straight out of grad school is one of the best ways to make academia healthy again!
Want to start your own lab out of grad school? Arc’s Science Fellows receive funding for a team of 2-4 people! Applications due Jan 15 from new-career scientists in Neurobiology or Immunology.
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
December 2, 2024 at 11:59 PM
Hiring more faculty straight out of grad school is one of the best ways to make academia healthy again!
Reposted by Chongyuan Luo
Want to start your own lab out of grad school? Arc’s Science Fellows receive funding for a team of 2-4 people! Applications due Jan 15 from new-career scientists in Neurobiology or Immunology.
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
November 27, 2024 at 12:58 AM
Want to start your own lab out of grad school? Arc’s Science Fellows receive funding for a team of 2-4 people! Applications due Jan 15 from new-career scientists in Neurobiology or Immunology.
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
Join Arc co-founder Patrick Hsu for an info session Fri 12/6 10 am PST. Register here: shorturl.at/r1cgD
Reposted by Chongyuan Luo
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
HiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact maps
Hi-C is a chromosome conformation capture assay used to study 3D genome organization. The recent development of single-cell Hi-C technologies has further enabled the examination of 3D chromatin organi...
www.biorxiv.org
November 26, 2024 at 12:39 PM
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...