Publications

Transcriptome and physiological analyses implicate multiple light signaling pathways in the control of solar tracking in sunflower

Chris Brooks, Hagop Atamian, and Stacey Harmer (2023) under revision

Myb-like transcription factors have epistatic effects on circadian clock function but additive effects on plant growth

Cassandra Hughes and Stacey Harmer (2023) under revision

XAP5 CIRCADIAN TIMEKEEPER regulates RNA splicing and the circadian clock by genetically separable pathways

Hongtao Zhang, Rod Kumimoto, Shajahan Anver, Stacey Harmer (2023) Plant Physiology

The circadian clock controls temporal and spatial patterns of floral development in sunflower

Carine Marshall, Veronica Thompson, Nicky Creux, and Stacey Harmer (2023) eLife

XAP5 CIRCADIAN TIMEKEEPER affects both DNA damage responses and immune signaling in Arabidopsis

Rod Kumimoto, Cory Ellison, Tania Toruño, Aurélie Bak, Hongtao Zhang, Clare Casteel, Gitta Coaker, and Stacey Harmer (2021) Frontiers in Plant Science

Flower orientation influences floral temperature, pollinator visits and plant fitness

Nicky Creux, Evan Brown, Austin Garner, Sana Saeed, Lane Scher, Srinidhi Holalu, Daniel Yang, Julin Maloof, Benjamin Blackman, and Stacey Harmer (2021) New Phytologist

A TILLING by sequencing approach to identify induced mutations in sunflower genes

Valentina Fanelli, Kathie Ngo, Veronica Thompson, Brennan Silva, Helen Tsai, Wilma Sabetta, Cinzia Montemurro, Luca Comai, and Stacey Harmer (2021) Scientific Reports

2015-2019

Circadian rhythms in plants

Nicky Creux and Stacey Harmer (2019) Cold Spring Harbor Perspectives in Biology

Arabidopsis JMJD5/JMJ30 acts independently of LUX ARRHYTHMO within the plant circadian clock to enable temperature compensation

Matt Jones, Kengo Morohashi, Erich Grotewold, and Stacey Harmer (2019) Front Plant Sci

Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions

Akiva Shalit-Kaneh, Rod Kumimoto, Vladimir Filkov, and Stacey Harmer (2018) PNAS

Growth-mediated plant movements - hidden in plain sight

Stacey Harmer and Chris Brooks (2017) Curr Opin Plant Biol

Circadian rhythms vary over the growing season and correlate with fitness components

Matthew Rubin, Marcus Brock, Amanda Davis, Zachary German, Mary Knapp, Steve Welch, Stacey Harmer, Julin Maloof, Seth Davis, and Cynthia Weinig (2017) Mol Ecology

The REVEILLE clock genes inhibit growth of juvenile and adult plants by control of cell size

Jennifer Gray, Akiva Shalit-Kaneh, Dalena Chu, Polly Hsu, and Stacey Harmer (2017) Plant Phys

YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance

Patricia Müller-Moulé, Kazu Nozue, Melissa Pytlak, Christine Palmer, Mike Covington, Andii Wallace, Stacey Harmer, and Julin Maloof (2016) PeerJ

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits

Hagop Atamian, Nicky Creux, Evan Brown, Austin Garner, Ben Blackman, and Stacey Harmer (2016) Science

Circadian regulation of hormone signaling and plant physiology

Hagop Atamian and Stacey Harmer (2016) Plant Mol Biol

A constitutively active allele of phytochrome B maintains circadian robustness in the absence of light

Matt Jones, Wei Hu, Suzanne Lithauer, Clark Lagarias, and Stacey Harmer (2015) Plant Phys

Reassess the t test - interact with all your data via ANOVA

Siobhan Brady, Meike Burow,Wolfgang Busch,Orjan Carlborg, Katherine Denby, Jane Glazebrook, Eric Hamilton, Stacey Harmer, Liz Haswell, Julin Maloof, Nathan Springer, and Dan Kliebenstein (2015) Plant Cell

2010-2014

Turning heads - the biology of solar tracking in sunflower

Joshua Vandenbrink, Evan Brown, Stacey Harmer, and Ben Blackman (2014) Plant Sci

Yeast X‐chromosome‐associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts

Shajahan Anver, Assen Roguev, Martin Zofall, Nevan Krogan, Shiv Grewal, and Stacey Harmer (2014) EMBO reports

Global profiling of the circadian transcriptome using microarrays

Polly Hsu and Stacey Harmer (2014) Methods Mol Biol

Wheels within wheels - the plant circadian system

Polly Hsu and Stacey Harmer (2014) Trends Plant Sci

Accurate timekeeping is controlled by a cycling activator in Arabidopsis

Polly Hsu, Upendra Devisetty, and Stacey Harmer (2013) eLife

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

Assaf Zemach, Yvonne Kim, Ping Hsieh, Devin Coleman-Derr,Leor Eshed-Williams, Ka Thao, Stacey Harmer, and Daniel Zilberman (2013) Cell

Circadian phase has profound effects on differential expression analysis

Polly Hsu and Stacey Harmer (2012) PLoS One

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 causes circadian clock defects

Matt Jones, Brian Williams, Jim McNicol, Craig Simpson, John Brown, and Stacey Harmer (2012) Plant Cell

Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis

Kazu Nozue, Stacey Harmer, and Julin Maloof (2011) Plant Physiology

REVEILLE8 and PSEUDO-REPONSE REGULATOR5 Form a Negative Feedback Loop within the Arabidopsis Circadian Clock

Reetika Rawat, Nozomu Takahashi, Polly Hsu, Matt Jones, Koby Schwartz, Michelle Salemi, Brett Phinney, and Stacey Harmer (2011) PLoS Genetics

JMJD5 Functions in concert with TOC1 in the Arabidopsis circadian system

Matt Jones and Stacey Harmer (2011) Plant Signal Behav

XAP5 CIRCADIAN TIMEKEEPER regulates ethylene responses in aerial tissues of Arabidopsis

Cory Ellison, Filip Vandenbussche, Dominique Van Der Straeten, and Stacey Harmer (2011) Plant Phys

Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis

Rachel Kerwin, Jose Jimenez-Gomez, Dan Fulop, Stacey Harmer, Julin Maloof, and Dan Kliebenstein (2011) Plant Cell

Jumonji domain protein JMJD5 functions in both the plant and human circadian systems

Matt Jones, Mike Covington, Luciano DiTacchio, Chris Vollmers, Satchin Panda, and Stacey Harmer (2010) PNAS

Plant biology in the fourth dimension

Stacey Harmer (2010) Plant Phys

2000-2009

The circadian system in higher plants

Stacey Harmer (2009) Ann Rev Plant Bio

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

Mike Covington, Julin Maloof, Marty Straume, Steve Kay, and Stacey Harmer (2008) Genome Biol

XAP5 CIRCADIAN TIMEKEEPER coordinates light signals for proper timing of photomorphogenesis and the circadian clock in Arabidopsis

Ellen Martin-Tryon and Stacey Harmer (2008) Plant Cell

The development of protein microarrays and their applications in DNA–protein and protein–protein interaction analyses of Arabidopsis transcription factors

Gong Wei, He Kun, Mike Covington, Dinesh-Kumar, Mike Snyder, Stacey Harmer, Yu-Xian Zhu, Xing Wang Deng (2008) Mol Plant

Mechanical stress induces biotic and abiotic stress responses via a novel cis-element

Justin Walley, Sean Coughlan, Matt Hudson, Mike Covington, Roy Kaspi, Gopalan Banu, Stacey Harmer, and Katie Dehesh (2007) PLoS Genetics

The circadian clock regulates auxin signaling and responses in Arabidopsis

Michael Covington and Stacey Harmer (2007) PLoS Bio

Rhythmic growth explained by coincidence between internal and external cues

Kazu Nozue, Mike Covington, Paula Duek, Séverine Lorrain, Christian Fankhauser, Stacey Harmer and Julin Maloof (2007) Nature

GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock

Karina Oliverio, María Crepy, Ellen Martin-Tryon, Raechel Milich, Stacey Harmer, Jo Putterill, Marcelo Yanovsky, and Jorge Casal (2007) Plant Phys

GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation

Ellen Martin-Tryon, Joel Kreps, and Stacey Harmer (2007) Plant Phys

Circadian regulation of global gene expression and metabolism

Stacey Harmer, Mike Covington, Oliver Blasing, and Mark Stitt (2006) Endogenous Plant Rhythms

Positive and negative factors confer phase-specific circadian regulation of transcription in Arabidopsis

Stacey Harmer and Steve Kay (2005) Plant Cell

Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock

Eva Farré, Stacey Harmer, Frank Harmon, Marcelo Yanovsky, and Steve Kay (2005) Current Biology

Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis

David Alabadi, Marcelo Yanovsky, Paloma Mas, Stacey Harmer, and Steve Kay (2002) Current Biology

Molecular bases of circadian rhythms

Satchin Panda, Stacey Harmer, and Steve Kay (2001) Ann Rev Cell Dev Bio

Orchestrated transcription of key pathways in Arabidopsis by the circadian clock

Stacey Harmer, John Hogenesch, Marty Straume, Hur-Song Chang, Bin Han, Tony Zhu, Xun Wang, Joel Kreps, and Steve Kay (2000) Science