ShihLab@LabShih

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

 Berkeley, CA
nature.berkeley.edu/shih-lab
Joined May 2019
13 Photos and videos
ShihLab retweeted
Corinne Scown@cdscown
Jun 15
Nice UCB study on the human health impacts of deploying carbon capture and sequestration, now out in @naturesustainab! Check out the paper here: rdcu.be/fopCu
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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. go.nature.com/4pw5cL1

Multiplexed profiling of transcriptional regulators in plant cells

Nature Biotechnology - ENTRAP-seq systematically links protein sequence to transcriptional output in a native plant context.

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Multiplexed profiling of transcriptional regulators in plant cells go.nature.com/4pw5cL1
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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.🌱🦠🧬 pubs.acs.org/doi/10.1021/acs…

Genetically Reprogramming Crops and Rhizobacteria for Nutritional Iron Biofortification

Abstract. Iron is a critical micronutrient for both plants and humans, yet its declining availability across agricultural systems threatens global food sec

pubs.acs.org
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Active learning enables discovery of transcriptional activators across fungal evolutionary space biorxiv.org/content/10.1101/… #biorxiv_genomic

Active learning enables discovery of transcriptional activators across fungal evolutionary space

Biological discovery and design are increasingly being guided by predictive models in place of costly experimentation. However, existing datasets are often biased by overrepresentation from model...

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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.
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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.
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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: biorxiv.org/content/10.1101/…
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Big news from Demirer lab: 4 research papers preprinted! Feedback welcomed: eCIS for plant protein delivery: tinyurl.com/mrx4d878 R2 for targeted insertion: tinyurl.com/5n73za6h Transient expression: tinyurl.com/38p2ud6w Chemotaxis assay: tinyurl.com/3nw9haes 👀⬇️
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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. biorxiv.org/content/10.1101/…
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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! biorxiv.org/content/10.1101/…
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Causes and consequences of experimental variation in Nicotiana benthamiana transient expression biorxiv.org/content/10.1101/… #biorxiv_plants
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Today the Shih Lab (@LabShih) presents ENTRAP-seq, a high-throughput assay for functional screening directly in plant cells.
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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. biorxiv.org/content/10.1101/…

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulatory domains play key roles in plant growth, development, and environmental responses. Massively parallel reporter assays in yeast and animal cells have enabled large-scale...

biorxiv.org
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ShihLab retweeted
Josh Cuperus@RNAnerd
13 May 2025
nature.com/articles/s41477-0…
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New OA Article: "Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-dependent synergy and antagonism" rdcu.be/elJ5z News & Views: "Cooperation and antagonism in Agrobacterium-mediated transformation" rdcu.be/elJ5F
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Happy to share our new publication out today in @NaturePlants where we quantitatively dissect synergy and antagonism that occurs during Nicotiana benthamiana transient agroinfiltration. Congrats to Simon, Matthew, Mitch and all other co-authors! nature.com/articles/s41477-0…

Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-d...

Nature Plants - Alamos et al. show that Agrobacterium engages in density-dependent interactions that dictate transformation efficiency and transgene expression. These findings enable a quantitative...

nature.com
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We also very much appreciate the associated News and Views article: nature.com/articles/s41477-0…
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