Chongyuan Luo @chongyuanluo.bsky.social · 30/01/2026We are excited to release a single-cell and spatial 3D epigenomic atlas of developing human basal ganglia and inhibitory neurons, part of our BICAN effort in collaboration with Mercedes Paredes, Jason Ernst, Eran Mukamel, Quan Zhu, Bogdan Pasaniuc. www.biorxiv.org/content/10.6... 000
Chongyuan Luo @chongyuanluo.bsky.social · 15/10/2025We 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... 011
Chongyuan Luo @chongyuanluo.bsky.social · 10/07/2025Congrats 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...elifesciences.orgThe impact of ambient contamination on demultiplexing methods for single-nucleus multiome experimentsAltmetric provides a collated score for online attention across various platforms and media.See more details 010
Chongyuan Luo @chongyuanluo.bsky.social · 23/06/2025Preprint 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. 021
Chongyuan Luo @chongyuanluo.bsky.social · 04/03/2025As 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 000
Chongyuan Luo @chongyuanluo.bsky.social · 04/03/2025assuming 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 000
Chongyuan Luo @chongyuanluo.bsky.social · 04/03/2025I 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 000
Chongyuan Luo @chongyuanluo.bsky.social · 24/02/2025Illumina 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 010
Chongyuan Luo @chongyuanluo.bsky.social · 10/02/2025Does 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...biorxiv.orgThe impact of ambient contamination on demultiplexing methods for single-nucleus multiome experimentsSample 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... 041
Reposted by Chongyuan LuoSri Kosuri @srikosuri.bsky.social · 08/02/2025It’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. 841009846
Reposted by Chongyuan LuoHyejung Won @hyejungwon.bsky.social · 27/01/20251/ 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...cell.comMassively parallel reporter assay investigates shared genetic variants of eight psychiatric disordersHigh-throughput experimental validation of genetic variants linked to eight psychiatric disorders reveals the regulatory mechanisms underlying variants with pleiotropic and disorder-specific effects. 54621
Chongyuan Luo @chongyuanluo.bsky.social · 24/01/2025Paperpile @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. 010
Chongyuan Luo @chongyuanluo.bsky.social · 22/01/2025Paperpile @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 100
Chongyuan Luo @chongyuanluo.bsky.social · 16/01/2025~20 yrs ago I chose bio major because bio requires the least amount of math but look where we are now 000
Reposted by Chongyuan LuoBenoit Bruneau @benoitbruneau.bsky.social · 13/01/2025our 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... 510127
Reposted by Chongyuan LuoNandita Garud @nanditagarud.bsky.social · 06/01/2025UCLA QCBIO is looking for its next director! Please consider applying! recruit.apo.ucla.edu/JPF10007recruit.apo.ucla.eduDirector, Institute for Quantitative and Computational BiosciencesUniversity of California, Los Angeles is hiring. Apply now! 02129
Chongyuan Luo @chongyuanluo.bsky.social · 06/01/2025Not 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. 010
Chongyuan Luo @chongyuanluo.bsky.social · 06/01/2025I 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 120
Chongyuan Luo @chongyuanluo.bsky.social · 31/12/2024the 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 000
Chongyuan Luo @chongyuanluo.bsky.social · 23/12/2024If 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. 110
Chongyuan Luo @chongyuanluo.bsky.social · 22/12/2024However, 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. 121
Chongyuan Luo @chongyuanluo.bsky.social · 22/12/2024bioRxiv has transformed the publication of biological research. All these tweaking of open access policy, not so much. 000
Chongyuan Luo @chongyuanluo.bsky.social · 09/12/2024The 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. 210
Chongyuan Luo @chongyuanluo.bsky.social · 02/12/2024Hiring more faculty straight out of grad school is one of the best ways to make academia healthy again! 031
Reposted by Chongyuan LuoArc Institute @arcinstitute.org · 27/11/2024Want 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 085
Reposted by Chongyuan LuoRui Yang @ruiyang.bsky.social · 26/11/2024Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps! www.biorxiv.org/content/10.1...biorxiv.orgHiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact mapsHi-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... 122
Chongyuan Luo @chongyuanluo.bsky.social · 01/12/2024First bsky post! What does “IS” stand for in the ISPCR step of Smart-seq? 020