Taihei Fujimori

PhD at UTokyo → Postdoc in the Bintu lab at Stanford / I am interested in single-cell chromatin organization mediated by epigenetic mechanisms.

[Taihei Fujimori @fjmrt]

New preprint! We studied how single-cell 3D chromatin structure changes under targeted epigenetic perturbations using multiplexed DNA FISH and synthetic biology tools, and found an intriguing relationship between chromatin compaction and epigenetic memory. https://t.co/6UHi86c6E7

[William J. Greenleaf @WJGreenleaf]

Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia! https://t.co/4zjMOlOgVV

[Josh Tycko @JoshTycko]

Our new paper on epigenome editing is out!

We mapped which effector domains regulate transcription across genomic, cell type and DNA-binding domain contexts. Then we built new gene repressor and activator tools with improved efficiency & deliverability

https://t.co/VqRLtNFey7

[Joydeb Sinha @sinha_joydeb]

Lastly, I would also like to give a shout out to Nate Hathaway’s lab @UNCPharmacy for writing a beautiful preview article elegantly describing our work. Please check it out here! : https://t.co/bEVaAJysMb (4/4)

[Joydeb Sinha @sinha_joydeb]

I'm thrilled to announce that my PhD thesis work from @BintuLab on how the H3.3K36M oncohistone disrupts the establishment of epigenetic memory is now out in the latest issue of @MolecularCell. https://t.co/O8t28MwM7q (1/4)

[Elphege Nora Lab at UCSF @ElphegeNoraLab]

First preprint from the lab 🚨

How can enhancers regulate target promoters across vast genomic distances, and what is the role of cohesin loop extrusion in the process?

https://t.co/l7bwPsTSkd

(1)

[Raeline Valbuena @rcvalbuena]

I’m amped to share our new work to decrypt transcriptional repressors, now on bioRxiv: https://t.co/BeKDmg3rUy
We paired deep mutational scans with machine learning to predict and even tune repressor activity. (1/8)

[Ichiro Hiratani @IchiroHiratani]

Our paper is out! Congrats to Saori Takahashi, Hiro Kyogoku, Tomo Kitajima, and everyone involved! We discovered a 2-step transition in DNA replication regulation accompanied by transient genome instability in early mouse embryos.
https://t.co/45qOCNarlB

[Nicole DelRosso @nicole_delrosso]

🧬How do transcriptional cofactors recognize which genes to regulate?🧬 Check out our new preprint from @fordycelab @BintuLab that tackles this question and provides the first-ever quantitative map of disordered transcriptional protein interactions (1/9) https://t.co/5UV8IafaHM

[Simon Gaudin @SimonMJGaudin]

Delighted to see our work https://t.co/jawirY5X5R from the Canzio lab @UCSF on how #cohesin-mediated enhancer-promoter interactions shape stochastic #Protocadherin choice profiles out @ScienceMagazine. #epigenetics #chromatin #DNAmethylation #LoopExtrusion #CTCF #3Dgenome. (1/8)

[Abby Thurm @abbythurm]

Do human RNA-binding proteins have modular regulatory domains that downregulate RNA lifetimes? Our preprint @BintuLab studying this question is now out on bioRxiv, where we indeed identify small domains in RBPs that potently induce RNA degradation! https://t.co/nOsgx1a3gA (1/9)

[Bintu Lab @BintuLab]

We are hiring a lab manager/research assistant! More details and how to apply here: https://t.co/zKZXALbT8k

[Taihei Fujimori @fjmrt]

Apparently, you can subscribe to brain organoids and stimulate them through a Python API for $500/mo. What would you do with them?
https://t.co/N2xcRdAZ5J

[Taihei Fujimori @fjmrt]

San Francisco is a city where 70-year-old streetcars share the roads with driverless cars.

[Prashant Bhat @_prashantbhat]

A long sought after hypothesis has been that organizing biomolecules in and around nuclear bodies is essential for functional RNA processing. We now provide direct evidence of this in @Nature for nuclear speckles and mRNA splicing. Check out this thread!

https://t.co/DoXSB7SINt

[Dr. Sedona Murphy @SedonaMurphy]

Seeking someone looking for a two-year postbac position to get my group up and running at Yale University! We will be utilizing chromatin tracing and other multiplexed imaging approaches to study the relationship between 3D genome organization and epigenetic memory in embryos!

[Dr. Sedona Murphy @SedonaMurphy]

So excited to finally see this out in its final form!!!

https://t.co/3q9X8KBclk

[Scott Coyle @CellRaiser_]

Our first paper is out in @CellCellPress! Led by @born2raisecell, we present a programmable reaction-diffusion system that generates synthetic protein waves, oscillations, and patterns for spatiotemporal circuit design and FM data-encoding in human cells. https://t.co/lNRtRdJAxx

[ElowitzLab @ElowitzLab]

Just posted a preprint on our new spatial genomic recording system, baseMEMOIR.
https://t.co/ef5i8FnIOw
Motivation: Cells divide, differentiate, and migrate to form exquisitely organized tissues. Reconstructing the dynamic histories of individual cells, including their lineage relationships and ancestral states, is essential for understanding how intrinsic and extrinsic signals generate tissues during development and in regenerative medicine.
Engineered genomic recording systems can reconstruct cell lineage histories from endpoint measurements. However, existing methods either require sequencing (disrupting spatial organization) or have been limited in memory size and scalability.
To address this need, @ChadlyDuncan, Kirsten Frieda, and others in the lab created a high memory capacity image-readable recording system termed baseMEMOIR.

[Takamasa Kudo @TakaKud0]

Our preprint on the development of PerturbView, an Optical Pooled Screening (OPS) technology, is out! Massive thanks to @eric_lubeck for driving the project with me, along with our fantastic mentors, Orit Rozenblatt-Rosen, @LeviAGarraway and Aviv Regev
https://t.co/MbijOGpwTX 1/

[Yodai Takei @yodai_takei]

Thrilled to receive @SciLifeLabPrize in my category! Thanks again for the amazing support during my PhD @LongCai_Lab @Caltech. I am also super excited for the future of the spatial multi-omics field! https://t.co/tYDRUrCIUq