Author

J. C. Pires

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 5 Plant Biology· 3 Pharmacology & Toxicology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 6 Organism:Arabidopsis· 4 Organism:plant (other)· 4 Assay:bulk RNA-seq· 3 Research Focus:cell type annotation· 2 Research Focus:chromatin & epigenetic regulation· 2 Assay:DNA methylation· 2 Approach:experimental assay· 2

Frequent Co-Authors

G. C. Conant· 4 shared P. P. Edger· 4 shared H. An· 3 shared J. D. Washburn· 2 shared J. M. Brose· 2 shared K. A. Bird· 2 shared M. E. Mabry· 2 shared M. E. Schranz· 2 shared

Activity by Year

2017-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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4 shared papersPlant Biology

G. C. Conant

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Author profile →

9 papers

Recent·Most cited

INTERPRETABLE MACHINE LEARNING UNVEILS KEY PREDICTORS AND DEFAULT VALUES IN AN EXPANDED DATABASE OF HUMAN IN VITRO DERMAL ABSORPTION STUDIES WITH PESTICIDES

D. A. Sarti, J. Wagner, F. Palma, H. Kalvan, M. F. Giachini, D. Lautenschalaeger, V. Lupianhez, J. C. Pires, M. Sales, P. M. de Faria, L. C. Bertomeu, M. Le Bras

This paper uses interpretable machine learning to identify key predictors and establish default dermal absorption values for pesticides based on in vitro human skin studies.

bioRxiv · May 11, 2023Pharmacology & Toxicology

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

K. P. Hendriks, C. Kiefer, I. A. Al-Shehbaz, C. D. Bailey, A. A. C. Hooft van Huysduynen, L. Nikolov, L. Nauheimer, A. R. Zuntini, D. A. German, A. Franzke, M. A. Koch, M. A. Lysak, O. Toro-Nunez, B. Ozudogru, V. R. Invernon, , Fore

This paper presents a comprehensive Brassicaceae phylogeny, identifies cytonuclear discordance due to hybridization, and proposes new tribes, providing a tool for biodiversity and plant biology studies.

bioRxiv · Sep 1, 2022Evolutionary Biology

Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

K. A. Bird, J. C. Pires, R. VanBuren, Z. Xiong, P. P. Edger

This study examines how dosage-sensitive genes in Brassica napus respond to homoeologous exchanges and whole-genome duplication, finding constrained expression responses and genomic imbalance.

bioRxiv · Nov 16, 2021Evolutionary Biology

Distinct C4 Sub-Types and C3 Bundle Sheath Isolation In The Paniceae Grasses

J. D. Washburn, J. Strable, P. Dickinson, S. S. Kothapalli, J. M. Brose, S. Covshoff, G. C. Conant, J. M. Hibberd, J. C. Pires

The paper examines C4 acid decarboxylase diversity in Paniceae grasses, showing species-specific transcript and enzyme activity patterns and developing a C3 bundle sheath isolation method.

bioRxiv · Sep 19, 2021Plant Biology

Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

X. Qi, H. An, T. E. Hall, C. Di, P. Blischak, M. T. W. McKibben, Y. Hao, G. C. Conant, J. C. Pires, M. S. Barker

The paper identifies candidate genes associated with domestication in Brassica rapa and finds that genes from ancient polyploidy are more diverse and linked to domestication.

bioRxiv · Oct 15, 2020Plant Biology

Surprising amount of stasis in repetitive genome content across the Brassicales

A. Beric, M. E. Mabry, A. E. Harkess, M. E. Schranz, G. C. Conant, P. P. Edger, B. C. Meyers, J. C. Pires

The paper investigates genome size evolution in Brassicales, finding no correlation between genome size and TE content or significant changes in TE landscapes after WGD.

bioRxiv · Jun 15, 2020 · PreprintEvolutionary Biology

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploidBrassica napus

K. A. Bird, C. Niederhuth, S. A. Ou, M. A. Gehan, J. C. Pires, Z. Xiong, R. VanBuren, P. P. Edger

This study investigates subgenome dominance in Brassica napus allopolyploids by replaying the evolutionary tape, finding consistent expression bias towards the C subgenome.

bioRxiv · Jan 27, 2020Evolutionary Biology

Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales

M. E. Mabry, J. M. Brose, P. D. Blischak, B. Sutherland, W. T. Dismukes, C. A. Bottoms, P. P. Edger, J. D. Washburn, H. An, J. C. Hall, M. R. McKain, I. Al-Shehbaz, M. S. Barker, M. E. Schranz, G. C. Conant, J. C. Pires

The paper infers phylogenies and places whole-genome duplication events in Brassicales using phylo-transcriptomics and genome survey sequencing.

bioRxiv · Oct 1, 2019Evolutionary Biology

Persistent homology demarcates a leaf morphospace

M. Li, H. An, R. Angelovici, C. Bagaza, A. Batushansky, L. Clark, V. Coneva, M. Donoghue, E. Edwards, D. Fajardo, H. Fang, M. Frank, T. Gallaher, S. Gebken, T. Hill, , D. H. Chitwood

This paper uses persistent homology to analyze leaf shapes from 182,707 leaves across 141 plant families, revealing phylogenetic and geographic differences in leaf morphology.

bioRxiv · Jun 20, 2017Plant Biology