Author

P. A. Haynes

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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Plant Biology· 4 Biochemistry· 3

Signature Assays, Organisms & Methods

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Assay:proteomics· 7 Approach:experimental assay· 5 Research Focus:differential expression· 4 Research Focus:cell type annotation· 3 Organism:plant (other)· 3 Research Focus:protein folding & dynamics· 3 Approach:statistical model· 3 Research Focus:benchmarking· 2

Frequent Co-Authors

B. J. Atwell· 4 shared D. C. L. Handler· 3 shared F. Masoomi-Aladizgeh· 2 shared K. S. Kamath· 2 shared A. Nawrocki· 1 shared D. C. Plett· 1 shared D. Multari· 1 shared F. Habibpourmehraban· 1 shared

Activity by Year

2020-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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4 shared papersPlant Biology

B. J. Atwell

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Author profile →

7 papers

Recent·Most cited

Unique and shared proteome responses of rice plants (Oryza sativa) to individual abiotic stresses

F. Habibpourmehraban, B. J. Atwell, P. A. Haynes

This study identifies stress-specific and shared proteome responses in rice plants to drought, salinity, and temperature stresses, revealing most responses are unique to individual stresses.

bioRxiv · Oct 19, 2022 · PreprintPlant Biology

Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat

F. Masoomi-Aladizgeh, K. S. Kamath, P. A. Haynes, B. J. Atwell

This study uses proteomic analysis of heat-exposed cotton pollen to identify heat stress responses and resilience mechanisms in wild cotton.

Plant, Cell & Environment · Feb 17, 2022Peer-reviewedPlant Biology

Patterns of gene expression in pollen of cotton (Gossypium hirsutum) indicate down-regulation as a feature of thermotolerance

F. Masoomi-Aladizgeh, M. J. McKay, Y. Asar, P. A. Haynes, B. J. Atwell

The paper examines gene expression patterns in cotton pollen under heat stress, finding down-regulation and changes in protein abundance that suggest developmental stage-specific vulnerabilities.

bioRxiv · Jun 6, 2021Plant Biology

An experimentally-derived measure of inter-replicate variation in reference samples: the same-same permutation methodology

D. C. L. Handler, P. A. Haynes

The paper introduces a method to estimate inter-replicate variability in proteomics experiments using permutation analysis, enabling tailored multiple testing corrections.

bioRxiv · May 13, 2021 · PreprintBiochemistry

The phosphoproteome of rice leaves responds to water and nitrogen supply

S. Hamzelou, V. J. Melino, D. C. Plett, K. S. Kamath, A. Nawrocki, M. R. Larsen, B. J. Atwell, P. A. Haynes

This study investigates how water and nitrogen supply affect the phosphoproteome of rice leaves, identifying phosphorylation changes in proteins related to membrane transport and metabolic processes.

bioRxiv · Mar 15, 2021Plant Biology

PeptideMind: applying machine learning algorithms to assess replicate quality in shotgun proteomic data

D. C. L. Handler, P. A. Haynes

PeptideMind assesses replicate quality in shotgun proteomics data by using machine learning to identify biasing replicates and visualize significance measures.

bioRxiv · Aug 20, 2020Biochemistry

Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae

L. Deng, D. C. L. Handler, D. Multari, P. A. Haynes

This study compares protein and peptide fractionation methods for proteome analysis in yeast, finding that FASP-HpH provides the highest protein identification when using a high-resolution mass spectrometer.

bioRxiv · Feb 13, 2020Biochemistry