Cahan Lab | at JHMI

The second major chunk of my Ph.D. is now online in Genome Biology! Brief recap: 🧵 genomebiology.biomedcentral.com/articles/10.11…

Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells: Stem Cell Reports cell.com/stem-cell-repo…

@ekernf01 diagnoses false discoveries in GRNs in our latest paper. Grateful to Dr. Andrianantoandro @CellSystemsCP and reviewers like @anthonygitter for their invaluable peer review. This is how peer review should be done! 📄🔗 cell.com/cell-systems/f… cell.com/cell-systems/f…

PACNet quickly measures transcriptional fidelity of engineered cells from bulk data. Robust to exp method, it also compares yours to previously published data. Led by Emily Lo, with Dan Peng @Jvquez12 @MoEbrahimkhani @ChulanKwonLab. See @stemcellreports dlvr.it/SsTwDJ

@ekernf01 @ekernf01's paper in collab with @alexisjbattle uses model-X knockoff to address a huge problem with GRNs: unacceptably high FPR. Finds that causal sufficiency (assumed by most GRN methods) is invalid, raising doubts on the reliability of GRN results and methods that rely on them

0. FIRST PREPRINT OF MY PhD IS OUT!!! biorxiv.org/content/10.110… We have a super weird take on error control in gene regulatory network inference. Let me borrow your eyeballs. 🧵

We are looking for new postdocs to join our team. Positions are fully funded and you can pursue your interest in technology development, biological questions, or understanding disease. jobrxiv.org/job/johns-hopk…

Congratulations to Dr. Emily Su on the defense of her thesis Computational Tools to Explore Cell Identity Transitions with Application to Cell Fate Engineering! Please remember us when you become famous!

by @ErnestArenasSWE tinyurl.com/2ajz58hy, @francis_szele tinyurl.com/43czpcck, @PZandstra & @HDKaul tinyurl.com/4p52jk9f 8/n

by A Thakor tinyurl.com/56ed6wv8, @NSC_BrainDamage tinyurl.com/48e22hpk. 7/n

@stemcellreports special issue on Computational Systems Biology guest edited by @cahanlab and @TreutleinLab includes editorial conversation with ChatGPT on the state of the field tinyurl.com/2tfhm35d. Thank you to all of the contributors: 1/n

Submit your research to Stem Cell Reports—the premier society journal for stem cell research and an open access forum communicating basic discoveries in stem cell research, in addition to translational and clinical studies @isscr @martinperajax hubs.li/Q01t6Bgt0

Friends, Im excited to share my work linking #GRNs with dynamic #signals via #agents. The #multiscale GARMEN showed how a master GRN can lead to different #tissue structures. We successfully tested signal and transcriptomic perturbation outcomes in vitro bit.ly/3T41hES

We are pleased to announce the call for papers for a new special issue on the clinical translation of PSCs, guest edited by Drs. Shinya Yamanaka and Kazuto Takayama of @CiRA_KU_E . To learn more and sumit - bit.ly/3V1AmLS. @ISSCR @martinperaJAX @CellPress

M Zamani @NganHuang & R Cheng @cahanlab @HopkinsMedicine ID-ed regulators of endothelial to mesenchymal transition. Exploring #Tgfb & substrate stiffness on #EndMT they found a Mesenchymal-to-endothelial reversion and linked populations to #atherosclerosis onlinelibrary.wiley.com/doi/10.1002/ad…

Single-cell papers that make the count matrices and cell type classifications easily available are 100% more likely to be cited by me. Cell type-specific signature genes are a bonus.