Carly Shanks – Plant Systems Biology @ The Coruzzi Lab

Carly Shanks

June 2025

A new paper published by the Coruzzi Lab titled "Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency" appears in a special focus issue of The Plant Cell, “Translational Research from Arabidopsis to Crop Plants and Beyond,” which recognizes the 25th anniversary of the publication of the Arabidopsis genome sequence. DOI: 10.1093/plcell/koaf093. https://academic.oup.com/plcell/article/37/5/koaf093/8129742 Congrats to Ji Huang and all authors on their tremendous work!

June 2024

A recent article by the Coruzzi lab and colleages in Chile identifing conserved metabolic pathways and convergent biochemical adaptations Atacama Desert plants was selected as the Editors Choice in the June 2024 Issue of the Journal of Experimental Botany

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

Journal of Experimental Botany, Volume 75, Issue 11, 7 June 2024, https://doi.org/10.1093/jxb/erae117

May 2024

The Plant Cell Article written by Coruzzi Lab Post Doc Carly Shanks and colleagues was featured in the May 2024 Issue celebtating the ASPB centennial anniversary.

Nitrogen sensing and regulatory networks: it's about time and space

The Plant Cell, Volume 36, Issue 5, May 2024
https://doi.org/10.1093/plcell/koae038

A new study published in Frontiers in Genetics with close collaborators at the Courant Institute of Mathematical Sciences constructs bipartite networks to more accurately predict causality.

Bipartite networks represent causality better than simple networks: evidence, algorithms, and applications

Front. Genet., 08 May 2024 Sec. Computational Genomics, https://doi.org/10.3389/fgene.2024.1371607

August 2023

NEW! preprint of the “Living Fossil” Wollemia nobilis genome available on BioRxiv

The genome of the Wollemi pine, a critically endangered “living fossil” unchanged since the Cretaceous, reveals extensive ancient transposon activity

Featured Press Releases for Wollemi Pine Article!

November 2022

NEW Frontiers article written by Coruzzi Lab Post Doc Carly Shanks and colleagues!

Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice

Front. Plant Sci., 25 November 2022
Sec. Plant Physiology
https://doi.org/10.3389/fpls.2022.1006044

October 2022

The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells

Our TARGET system is published in as part of the Methods in Molecular Biology book series on Transcription Factor Regulatory Networks. (MIMB,volume 2594)

Transcription Factor Regulatory Networks pp 1–12 Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi & Bastiaan O. R. Bargmann Protocol First Online: 21 October 2022

DOI: 10.1007/978-1-0716-2815-7_1

December 2021

Our recent paper

Plant ecological genomics at the limits of life in the Atacama Desert

has been cited by PNAS, to be in the top 5% of their Altmetric Attention Score. This score provides an indicator of the amount of attention that a PNAS article has received. So far, our paper has been written about in 37 news stories from 30 outlets!

November 2021

NEW PNAS paper published on research led by collaborator Dr. Rodrigo A. Gutierrez, in Chile. Thank you for letting us join you on this 10- year journey!

Plant ecological genomics at the limits of life in the Atacama Desert

Featured Press Releases for PNAS Article!

HuffPost

Daily Beast

Genetic Engineering & Biotechnology News

October 2021

NSF's Research News Post! NSF PGRP NutriNet Project
Machine learning uncovers 'genes of importance' in agriculture

September 2021

Cheng et. al., (2021) Nature Communications Paper

“Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships.”

Click here to read the article on
Nature Communications!

Click here to read the wonderful NYU Press Release!

May 2020

PNAS Article: "Nutrient dose-responsive transcriptome changes driven by Michaelis–Menten kinetics underlie plant growth rates" on PNAS!

March 2020

Press release on NLP7, congratulations to Alvarez and Schinke et al.

Click Here to find out more!

April 2019

Gloria Coruzzi is elected into NAS!

Click Here to find out more!

coruzzilab Follow

Plant Systems Biology lab @nyuniversity. Account run by the people in the lab. Opinions are our own.

coruzzilab @coruzzilab ·

4 Jun

The Coruzzi Lab was featured in an article written by NYU News: "Artificial Intelligence and Genetics Can Help Farmers Grow Corn with Less Fertilizer". https://nyu.edu/about/news-publications/news/2025/may/ai-nue-regulons.html…Click to see Maize growing in our Rooftop Zegar Greenhouse!

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coruzzilab @coruzzilab ·

4 Jun

Check out our most recent paper, featured in the May 2025 edition of @ThePlantCell, highlighting a "Focus on Translational Research from Arabidopsis to Crop Plants and Beyond"

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coruzzilab @coruzzilab ·

13 Sep

This presentation is a tribute to Joe Key for his vision and leadership at the frontier of plant molecular biology, both scientifically and for community building. We are grateful for his vision and mourn his passing on Aug. 19, 2024. Gloria Coruzzi, NYU https://coruzzilab.bio.nyu.edu/wp-content/uploads/2024/09/Joe-Key-Tribute-by-Coruzzi_NYU.pdf

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coruzzilab @coruzzilab ·

27 Jun 2024

On May 17th, 2024 the @nyuniversity Annual Genome Symposium, hosted by the Center for Genomics and Systems Biology, honored the scientific achievements, life & career of dear friend, visionary, entrepreneur & mentor Dr. Philip Benfey. Recording Link:

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coruzzilab @coruzzilab ·

22 Sep 2023

Solved: The Enigma of the ‘Living Fossil’ Tree Preserved for 66 Million Years https://vervetimes.com/solved-the-enigma-of-the-living-fossil-tree-preserved-for-66-million-years/

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