ShihLab

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 go.nature.com/4pw5cL1

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/ac…

Active learning enables discovery of transcriptional activators across fungal evolutionary space biorxiv.org/content/10.110… #biorxiv_genomic

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/10.110…

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.

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.

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 👀⬇️

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/10.110…

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/10.110…

Causes and consequences of experimental variation in Nicotiana benthamiana transient expression biorxiv.org/content/10.110… #biorxiv_plants

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

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/10.110…

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

We also very much appreciate the associated News and Views article: nature.com/articles/s4147…

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/s4147…