Chaolin Zhang
@chaolinzhang
associate prof of systems bio at columbia university; networking in the rna world; go genome wide, for single nucleotide. 行胜于言. 📢 hiring students & postdocs
Four papers from the lab this year so far, a few more to go. These papers are a good reflection of our venture into engineering RNA regulation for research and therapeutics. Contact me if interested in this research direction. #RNA #engineering #PrecisionMedicine #PostDoc…
Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @CellCellPress, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. sciencedirect.com/science/articl…
We are excited to bring to you the Virtual Cell Challenge, a new benchmark initiative from the @arcinstitute to evaluate predictive models of cellular response to perturbation.
Register today for the Virtual Cell Challenge and use AI to solve one of biology’s most complex problems. Announced in @CellCellPress, the competition is hosted by Arc Institute and sponsored by @nvidia, @10xGenomics, and @UltimaGenomics.
Look forward to reading it!
Happy to introduce AlphaGenome, @GoogleDeepMind's new AI model for genomics. AlphaGenome offers a comprehensive view of the human non-coding genome by predicting the impact of DNA variations. It will deepen our understanding of disease biology and open new avenues of research.
Excited to report that our work to infer neuron type specific splicing-regulatory networks and splicing factor activities is now published in @CellReports. Led by a recent graduated PhD student @MoakleyDan. See 🧵⬇️. cell.com/cell-reports/f… @ColumbiaPS @ColumbiaSysBio #rna…
1/ Very happy to share that our preprint is now online! Check it out here: biorxiv.org/content/10.110… In the study, we model RNA alternative splicing regulation in the neocortex and validate both neuron type-specific and type-orthogonal regulatory programs. Read on for a summary!
Excited to announce a 2 week Cold Spring Harbor Asia (CSHA) summer course on Computational Genomics Aug 9-23, co organized by Jingyi Jessica Li @jsb_ucla, Qiangfeng Cliff Zhang, and myself. Application deadline June 8. @cshlcourses @CSHANews csh-asia.org/?content/2818. CSHA is…
A set of non-coding genetic variants -- mutations in RNA genes-- cause neurodevelopmental disorders by disrupting alternative splicing across the genome nature.com/articles/s4158…
Excited to share our new paper on Nature - how Ku accommodates Alu expansion in primates by binding to dsRNA, providing a clue for both the high levels of Ku and its essentiality in human cells. Thank @chaolinzhang @hchung03 @LenaSteckelberg More to come nature.com/articles/s4158…
Thank @LomvardasLab for the shout out! This is a great collaboration with @zha_lab! I guess #RNA always comes in to play a role when one does not expect them to - in this case Ku turns out to be the first (non-canonical) RBP I know of that co-evolves with Alu expansion!
nature.com/articles/s4158… Awesome new paper from Shan Za and @ColumbiaBiochem and systems biology colleague Chaolin Zhang @chaolinzhang
Happy to share our update to LeafCutter, which allows the study of unproductive splicing from short-read RNA-seq. We report findings from analysis of 3 large datasets (GTEx, multi-tissue development in 7 species, Alzheimer brains from AD FunGen consortium). See thread by Carlos.
We are excited to share our new preprint on LeafCutter2! Our new method clusters, quantifies, and classifies splice junctions and intron clusters according to their molecular functionality (e.g., protein-coding or NMD-splicing). @yang_i_li doi.org/10.1101/2025.0…
Given some recent publications regarding #RNA #Splicing prediction using #DeepLearning we decided to assess some of those claims with surprising findings that have to do more with the target function you chose… biociphers.wordpress.com/2025/04/09/tis…
In this study, Bangru et al. describe a regulatory switch that controls hepatocyte polyploidization and maturation through the activation of an RNA alternative splicing program that promotes cytokinesis failure and binucleation. Learn more here: ➡️ tinyurl.com/gd352129
Excited to share our latest work! We asked if and how TDP-43 regulates RNA transport in neurons and if this is misregulated in ALS. We found that it works to keep RNAs *out* of neurites, and that loss of TDP-43 activity results in specific RNAs aberrantly accumulating there.
Found this card outside my office this morning - "#RNA has #U in it". Someone is reminding me to hold on? I guess I should continue my @NIH grant reviews, although they stopped giving grants...
Precise RNA targeting with CRISPR–Cas13d go.nature.com/4gEn95x
Grateful to have the opportunity to contribute to the unexpected discovery! The first #RBP I know (a noncanonical one!) that has co-evolved to accommodate #Alu expansion in primates. It surprisingly binds to a single Alu inserted into genes in the antisense orientation.…
Exciting results! Using AID-Degron system, Dr. Yimeng Zhu found that Ku suppresses RNA-mediated innate immunity to accommodate Alu-expansion in primates - solving the misery of Ku essentiality in human cells! Thank@chaolinzhang biorxiv.org/content/10.110…
People routinely use Venn diagrams to show genes expressed in different conditions, such as cell types, and argue for cell-type specific expression based on the imperfect overlap. This is wrong and reflects a lack of the very basics of statistics. You can have imperfect overlap…