ShihLab

Twitter of the Lab of Dr. Patrick Shih at UC Berkeley

[ShihLab @LabShih]

What principles of TF activity have survived a billion years of evolution?

New Shih lab preprint! We used ENTRAP-seq to map activation and repression domains across Arabidopsis TFs and compared their activity in plants and yeast .

🍄⚖️🌱

https://t.co/uNLrS0hmoK

[Corinne Scown @cdscown]

Nice UCB study on the human health impacts of deploying carbon capture and sequestration, now out in @naturesustainab! Check out the paper here: https://t.co/yRnskWJoXU

[ShihLab @LabShih]

Our lab's new paper is out!

We introduce ENTRAP-seq, a high-throughput in planta assay for multiplexed profiling of protein-coding libraries. Using ENTRAP-seq and machine learning, we discovered transcriptional regulators from ~1,500 plant viral genomes.

https://t.co/RTNWcYzXtO

[Nature Biotechnology @NatureBiotech]

Multiplexed profiling of transcriptional regulators in plant cells https://t.co/JfLUA0nGZm

[Christopher Dundas @C_M_Dundas]

Excited to share our lab’s first publication at UGA!
PhD student Taden Welsh's new perspective highlights how plant + bacterial synthetic biology could enhance iron mobilization for food crop fortification.🌱🦠🧬
https://t.co/zCTvCmYhA0

[bioRxiv Genomics @biorxiv_genomic]

Active learning enables discovery of transcriptional activators across fungal evolutionary space https://t.co/SGxFIaPwJk #biorxiv_genomic

[ShihLab @LabShih]

Functional annotations from model organisms are insufficient for robust evolutionary predictions. Active learning across evolutionary space enables generalizable models to accelerate discovery in understudied branches of life.

Preprint: https://t.co/FVDXUScV4U

[ShihLab @LabShih]

Biological diversity beyond model organisms is poorly represented in ML training datasets.

Our new preprint uses a high-throughput assay and active learning to discover and characterize gene regulation in non-model organisms.

[ShihLab @LabShih]

Our study shows that existing models perform poorly on sequences from non-model organisms because they are out-of-distribution relative to sequences in model species.

[Gözde S. Demirer @Demirer_GozdeS]

Big news from Demirer lab: 4 research papers preprinted! Feedback welcomed:
eCIS for plant protein delivery: https://t.co/TYKrZNvBWR
R2 for targeted insertion: https://t.co/sYyqiriR7e
Transient expression: https://t.co/D7UmIeKaMo
Chemotaxis assay: https://t.co/poIANSvRsQ
👀⬇️

[Conor McClune @conor_mcclune]

A truly enabling new approach by Tara Lowensohn, @WillCody_12 and @Sattely_lab to probe plant genetics at scale.

Single-gene-per-cell delivery coupled to an effective transcriptional selection system.

Libraries in plants.

https://t.co/JfLtsLOSjb

[ShihLab @LabShih]

Check out our new preprint! We examined sources of variability of transgene expression in N. benthamiana agroinfiltration and ways to minimize it. Graduate student Sophia Tang observed FP expression in >1,800 plants over the course of nearly 3 years! https://t.co/dAYyhwrqRD

[bioRxiv Plant Bio @biorxiv_plants]

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression https://t.co/Fa0K5Akado #biorxiv_plants

[Lucas Waldburger @LucasWaldburger]

Today the Shih Lab (@LabShih) presents ENTRAP-seq, a high-throughput assay for functional screening directly in plant cells.

[ShihLab @LabShih]

We're excited to share another work from our lab this week. We present ENTRAP-seq, the first massively parallel reporter assay to characterize protein-coding libraries in plants. Congrats to Simon, Lucas, and all other co-authors.

https://t.co/S3gqsCJjp3

[Josh Cuperus @RNAnerd]

https://t.co/hscVezUEg4

[Nature Plants @NaturePlants]

New OA Article: "Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-dependent synergy and antagonism" https://t.co/qUkht3HYKb

News & Views: "Cooperation and antagonism in Agrobacterium-mediated transformation" https://t.co/VQ7MvFQTmI