We 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...
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...
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.
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
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
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...
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.
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...
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
~20 yrs ago I chose bio major because bio requires the least amount of math but look where we are now
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...
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.
I don't know whether different NIH institutes treat NOSI differently. Maybe some ICs give strong priorities to proposals responding to NOSIs...
My guess is no. The best we can do is to remind the reviewers on the aim page. what I heard from several POs is that many NOSIs had no grant funded, which shows how underwhelming the mechanism is
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
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.
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.
Hiring more faculty straight out of grad school is one of the best ways to make academia healthy again!
Uche Medoh and Jingtian Zhou
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
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps!
www.biorxiv.org/content/10.1...
First bsky post!
What does “IS” stand for in the ISPCR step of Smart-seq?
congress has long had interested in moving scientists and money to mid west. what’s interesting is I am hearing more often about “geographical diversity” from NIH personnel
