Data – Plant Systems Biology @ The Coruzzi Lab

Coruzzi Lab: Published Nitrogen Data Sets

Datasets	PubMed	Experiment Platform	Link to Data
Cheng CY Nat Commun 2021	Pubmed PDF	RNA-seq	GEO SRA
Brooks MD Plant Physiology 2021	Pubmed PDF	RNA-seq	GEO SRA
Alvarez Nat Commun. 2020	Pubmed PDF	RNA-seq	SRA
Brooks Nat Commun. 2019	Pubmed PDF	RNA-seq	SRA SRA2 GEO GEO2
Heerah Plant Physiology 2019	Pubmed PDF	Affymetrix	GEO
Varala PNAS 2018	Pubmed PDF	RNA-seq	GEO SRA
Ristova Sci Signaling 2016	Pubmed PDF	Affymetrix	GEO
Doidy BMC Genomics 2016	Pubmed PDF	Affymetrix	GEO
Obertello Plant Physiol 2015	Pubmed PDF	Affymetrix	GEO
Li Genome Biol 2015	Pubmed PDF	Affymetrix & Chip-seq	GEO , SRA
Medici Nat Commun 2015	Pubmed PDF	Affymetrix	GEO
Para PNAS 2014	Pubmed PDF	Affymetrix	GEO
Vidal BMC Genomics 2013	Pubmed PDF	Affymetrix , RNA-seq	GEO , SRA
Gifford PLoS Genet 2013	Pubmed PDF	Affymetrix	GEO
Bargmann MOL PLANT 2013	Pubmed PDF	Affymetrix	GEO
Ruffel PNAS 2011	Pubmed PDF	Affymetrix	GEO
Widiez PNAS 2011	Pubmed PDF	Affymetrix	GEO
Krouk Genome Biology 2010	Pubmed PDF	Affymetrix	GEO
Obertello BMC Systems Biology 2010	Pubmed PDF	Affymetrix	GEO
Thum BMC Systems Biology 2008	Pubmed PDF	Affymetrix	ArrayExpress
Gutierrez PNAS 2008	Pubmed PDF	Affymetrix	NASC
Gifford PNAS 2008	Pubmed PDF	Affymetrix	GEO
Wang Plant Physiology 2007	Pubmed PDF	Affymetrix	NASC
Gutierrez Genome Biology 2007	Pubmed PDF	Affymetrix	ArrayExpress
Palenchar Genome Biology 2004	Pubmed PDF	Affymetrix	Download
Thum Genome Biology 2004	Pubmed PDF	Affymetrix	ArrayExpress
Wang Plant Physiology 2004	Pubmed PDF	Affymetrix	NASC

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!

Genetic Engineering & Biotechnology News

Technology Networks

Cosmos Magazine

Daily Mail (UK)

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 ·

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

Reply on Twitter 1834614911273410837 Retweet on Twitter 1834614911273410837 2 Like on Twitter 1834614911273410837 6 Twitter 1834614911273410837

coruzzilab @coruzzilab ·

27 Jun

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:

Reply on Twitter 1806370695938519313 Retweet on Twitter 1806370695938519313 4 Like on Twitter 1806370695938519313 5 Twitter 1806370695938519313

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/

Reply on Twitter 1705226445868474608 Retweet on Twitter 1705226445868474608 Like on Twitter 1705226445868474608 Twitter 1705226445868474608

coruzzilab @coruzzilab ·

22 Sep 2023

Ancient Wollemi Pine: A Living Fossil Threatened with Extinction in Australia

https://www.world-today-news.com/ancient-wollemi-pine-a-living-fossil-threatened-with-extinction-in-australia/

Reply on Twitter 1705226184915620166 Retweet on Twitter 1705226184915620166 Like on Twitter 1705226184915620166 Twitter 1705226184915620166

coruzzilab @coruzzilab ·

22 Sep 2023

"Living Fossil" Wollemi Pine Is Ancient, Inbred, And In A Lot Of Trouble

Reply on Twitter 1705225972872581442 Retweet on Twitter 1705225972872581442 Like on Twitter 1705225972872581442 Twitter 1705225972872581442

Load More