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All Outputs (8)

Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2 (2023)
Journal Article
Tidy, A., Abu Bakar, N., Carrier, D., Kerr, I. D., Hodgman, C., Bennett, M. J., & Swarup, R. (2024). Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2. Plant Physiology, 194(1), 422-433. https://doi.org/10.1093/plphys/kiad506

AUXIN RESISTANCE4 (AXR4) regulates the trafficking of auxin influx carrier AUXIN1 (AUX1), a plasma-membrane protein that predominantly localizes to the endoplasmic reticulum (ER) in the absence of AXR4. In Arabidopsis (Arabidopsis thaliana), AUX1 is... Read More about Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2.

Arabidopsis antibody resources for functional studies in plants (2020)
Journal Article
Oh, J., Wilson, M., Hill, K., Leftley, N., Hodgman, C., Bennett, M. J., & Swarup, R. (2020). Arabidopsis antibody resources for functional studies in plants. Scientific Reports, 10(1), Article 21945. https://doi.org/10.1038/s41598-020-78689-1

© 2020, The Author(s). Here we report creation of a unique and a very valuable resource for Plant Scientific community worldwide. In this era of post-genomics and modelling of multi-cellular systems using an integrative systems biology approach, bett... Read More about Arabidopsis antibody resources for functional studies in plants.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development (2019)
Journal Article
Gilbert, J., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., …Twycross, J. (2019). Gsmodutils: a python based framework for test-driven genome scale metabolic model development. Bioinformatics, 35(18), 3397-3403. https://doi.org/10.1093/bioinformatics/btz088

© 2019 The Author(s) 2019. Published by Oxford University Press. Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-stat... Read More about Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

The logic of the floral transition: reverse-engineering the switch controlling the identity of lateral organs (2017)
Journal Article
Dinh, J., Farcot, E., & Hodgman, C. (in press). The logic of the floral transition: reverse-engineering the switch controlling the identity of lateral organs. PLoS Computational Biology, 13(9), Article e1005744. https://doi.org/10.1371/journal.pcbi.1005744

Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the quest... Read More about The logic of the floral transition: reverse-engineering the switch controlling the identity of lateral organs.

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize (2017)
Journal Article
Oka, R., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., …Stam, M. (2017). Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology, 18, Article 137. https://doi.org/10.1186/s13059-017-1273-4

© 2017 The Author(s). Background: While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the... Read More about Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles (2017)
Journal Article
Casbas Pinto, F., Ravipati, S., Barrett, D. A., & Hodgman, C. (2017). A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles. Metabolomics, 13(7), Article 81. https://doi.org/10.1007/s11306-017-1214-y

Introduction It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations. Objectives This work simplifies this process. Methods A method has been developed to query an online holistic lipid metabolic netwo... Read More about A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles.

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium (2015)
Journal Article
Humphreys, C. M., McLean, S., Schatschneider, S., Millat, T., Henstra, A. M., Annan, F. J., …Minton, N. P. (2015). Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genomics, 16(1), Article 1085. https://doi.org/10.1186/s12864-015-2287-5

© 2015 Humphreys et al. Background: Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the so... Read More about Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.