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List of works by James Whelan

A Casparian strip domain-like gene, CASPL, negatively alters growth and cold tolerance

scientific article published on 24 September 2015

A Functional Antagonistic Relationship between Auxin and Mitochondrial Retrograde Signaling Regulates Alternative Oxidase1a Expression in Arabidopsis

scientific article published in 2014

A Mitochondrial LYR Protein Is Required for Complex I Assembly

scientific article published on 10 October 2019

A Transcriptomic Signature of Mouse Liver Progenitor Cells

scientific article published on 03 October 2016

A dual-targeted purple acid phosphatase in Arabidopsis thaliana moderates carbon metabolism and its overexpression leads to faster plant growth and higher seed yield

article

A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch

scientific article published on 28 February 2018

A membrane-bound NAC transcription factor, ANAC017, mediates mitochondrial retrograde signaling in Arabidopsis

scientific article published on 17 September 2013

A molecular link between mitochondrial preprotein transporters and respiratory chain complexes ⬇️

scientific article published on October 16, 2012

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.

scientific article published on 31 October 2016

A transcription factor OsbHLH156 regulates Strategy II iron acquisition through localising IRO2 to the nucleus in rice

scientific article published on 01 November 2019

A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction

scientific article published on 15 January 2004

ACONITASE 3 is part of theANAC017 transcription factor-dependent mitochondrial dysfunction response

scientific article published on 01 August 2021

ANAC017 Coordinates Organellar Functions and Stress Responses by Reprogramming Retrograde Signaling

article

Accumulation of endogenous peptides triggers a pathogen stress response in Arabidopsis thaliana

scientific article published on 01 November 2018

Accumulation of newly synthesized F1 in vivo in arabidopsis mitochondria provides evidence for modular assembly of the plant F1Fo ATP synthase

scientific article published on 6 June 2012

Acquisition, conservation, and loss of dual-targeted proteins in land plants.

scientific article

AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

article

Alternative Oxidase Is Positive for Plant Performance.

scientific article

Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

scientific article published on 25 September 2018

Alternative oxidase isoforms are differentially activated by tricarboxylic acid cycle intermediates.

scientific article published on 5 December 2017

An in silico analysis of the mitochondrial protein import apparatus of plants ⬇️

scientific article

An mRNA Splice Variant of the AFX Gene with Altered Transcriptional Activity ⬇️

scientific article (publication date: 8 March 2002)

Analysis of Posttranslational Activation of Alternative Oxidase Isoforms

scientific article published on 8 June 2017

Analysis of the alternative oxidase promoters from soybean

scientific article published on 9 October 2003

Analysis of the rice mitochondrial carrier family reveals anaerobic accumulation of a basic amino acid carrier involved in arginine metabolism during seed germination

scientific article published on 18 August 2010

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

scientific article

Anterograde and retrograde regulation of nuclear genes encoding mitochondrial proteins during growth, development, and stress

scientific article published on 07 April 2014

Approaches to defining dual-targeted proteins in Arabidopsis

scientific article published on 11 December 2008

Arabidopsis DGD1 SUPPRESSOR1 Is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis

scientific article published on 22 May 2019

Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria

scientific article published on 01 October 2001

Assessing Modularity Using a Random Matrix Theory Approach ⬇️

scientific article published on September 26, 2011

AtWRKY40 and AtWRKY63 modulate the expression of stress-responsive nuclear genes encoding mitochondrial and chloroplast proteins

scientific article

Bioenergetic differences selectively sensitize tumorigenic liver progenitor cells to a new gold(I) compound

scientific article

Characterization of a novel β-barrel protein (AtOM47) from the mitochondrial outer membrane of Arabidopsis thaliana

scientific article

Characterization of the Import Pathway of the FAd Subunit of Mitochondrial ATP Synthase into Isolated Plant Mitochondria

article

Characterization of the preprotein and amino acid transporter gene family in Arabidopsis

scientific article published on 10 November 2006

Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development

scientific article published on 23 February 2007

Characterization of the targeting signal of dual-targeted pea glutathione reductase

scientific article published in October 2003

Cloning and characterization of AtNUDT13, a novel mitochondrial Arabidopsis thaliana Nudix hydrolase specific for long-chain diadenosine polyphosphates

scientific article

Cloning of an additional cDNA for the alternative oxidase in tobacco.

scientific article

Cloning of ndhK from soybean chloroplasts using antibodies raised to mitochondrial complex I

scientific article published on December 1, 1992

Cloning, analysis and inactivation of the ndhK gene encoding a subunit of NADH quinone oxidoreductase from Anabaena PCC 7120.

scientific article published in August 1996

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana ⬇️

scientific article published on November 24, 2010

Community recommendations on terminology and procedures used in flooding and low oxygen stress research.

scientific article published on 9 March 2017

Comparison of Transcriptional Changes to Chloroplast and Mitochondrial Perturbations Reveals Common and Specific Responses in Arabidopsis ⬇️

scientific article published on December 24, 2012

Comprehensive Mitochondrial Metabolic Shift during the Critical Node of Seed Ageing in Rice

scientific article

Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes

scientific article

Coordinating metabolite changes with our perception of plant abiotic stress responses: emerging views revealed by integrative-omic analyses

scientific article

Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment

scientific article published on 04 February 2022

Cyclin-dependent kinase E1 (CDKE1) provides a cellular switch in plants between growth and stress responses

scientific article published on 10 December 2012

Decreasing electron flux through the cytochrome and/or alternative respiratory pathways triggers common and distinct cellular responses dependent on growth conditions.

scientific article published on 6 November 2014

Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings

scientific article published in July 2009

Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets

scientific article

Defining the mitochondrial stress response in Arabidopsis thaliana

scientific article published on 24 July 2009

Determining Degradation and Synthesis Rates of Arabidopsis Proteins Using the Kinetics of Progressive 15N Labeling of Two-dimensional Gel-separated Protein Spots ⬇️

scientific article published on January 3, 2012

Differential Gene Expression and Subcellular Targeting of Arabidopsis GlutathioneS-Transferase F8 Is Achieved through Alternative Transcription Start Sites

scientific article published in Journal of Biological Chemistry

Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia

scientific article

Differentially expressed DNA sequences following recovery from unilateral testicular torsion in rat

scientific article published on 01 February 2001

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence

scientific article published on 15 October 2016

Dual and dynamic intracellular localization of Arabidopsis thaliana SnRK1.1.

scientific article published on 01 April 2019

Dual location of the mitochondrial preprotein transporters B14.7 and Tim23-2 in complex I and the TIM17:23 complex in Arabidopsis links mitochondrial activity and biogenesis

scientific article published in 2012

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

scientific article published on 12 November 2016

Environmental stresses inhibit and stimulate different protein import pathways in plant mitochondria

scientific article published on July 2003

Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa

scientific article

Evidence for Ancient Origins of Bowman-Birk Inhibitors from Selaginella moellendorffii

scientific article published on 14 March 2017

Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis

scientific article published on 29 November 2011

Evidence for a link between translocation and processing during protein import into soybean mitochondria

article

Evidence for interactions between the mitochondrial import apparatus and respiratory chain complexes via Tim21-like proteins in Arabidopsis.

scientific article published on 11 March 2014

Evolution of Protein Import Pathways

scientific article published in 2012

Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity

scientific article published on 14 November 2008

Exploring ligand recognition, selectivity and dynamics of TPR domains of chloroplast Toc64 and mitochondria Om64 fromArabidopsis thaliana

article

Exploring multicollinearity using a random matrix theory approach

scientific article published in January 2012

Exploring the function-location nexus: using multiple lines of evidence in defining the subcellular location of plant proteins

scientific article

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.

scientific article published on 15 September 2017

Functional and composition differences between mitochondrial complex II in Arabidopsis and rice are correlated with the complex genetic history of the enzyme

scientific article published on 19 November 2009

Functional characterization of the rice SPX-MFS family reveals a key role of OsSPX-MFS1 in controlling phosphate homeostasis in leaves

scientific article published on 17 July 2012

Functional definition of outer membrane proteins involved in preprotein import into mitochondria

scientific article published in 2007

GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress

scientific article published on 01 March 2022

Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2.

scientific article

Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana

scientific article published on 16 November 2007

Global transcriptome analysis of AtPAP2--overexpressing Arabidopsis thaliana with elevated ATP

scientific article

Glutaredoxin S15 Is Involved in Fe-S Cluster Transfer in Mitochondria Influencing Lipoic Acid-Dependent Enzymes, Plant Growth, and Arsenic Tolerance in Arabidopsis.

scientific article published on 15 December 2015

How do plants make mitochondria?

scientific article published on 14 September 2012

How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis

scientific article published on October 2013

Identification of OsbHLH133 as a regulator of iron distribution between roots and shoots in Oryza sativa

scientific article published on 24 July 2012

Identification of a dual-targeted protein belonging to the mitochondrial carrier family that is required for early leaf development in rice

scientific article published on 14 February 2013

Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa

scientific article

Identification of a novel mitochondrial protein, short postembryonic roots 1 (SPR1), involved in root development and iron homeostasis in Oryza sativa

article

Identification of signals required for import of the soybean F(A)d subunit of ATP synthase into mitochondria

scientific article

Import of precursor proteins into mitochondria from soybean tissues during development

article

Import of the mammalian cytochrome P450 (scc) precursor into plant mitochondria

scientific article published on 01 February 1994

In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis

scientific article published on 9 September 2011

Inactivation of Mitochondrial Complex I Induces the Expression of a Twin Cysteine Protein that Targets and Affects Cytosolic, Chloroplastidic and Mitochondrial Function.

scientific article published on 29 January 2016

Induction of alternative oxidase synthesis by herbicides inhibiting branched-chain amino acid synthesis

scientific article published in 1997

Interaction between hormonal and mitochondrial signalling during growth, development and in plant defence responses

scientific article

Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status

scientific article published on 3 March 2014

Intracellular gene transfer: reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochrome c oxidase

scientific article

Investigations on the in vitro import ability of mitochondrial precursor proteins synthesized in wheat germ transcription-translation extract

scientific article

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

scientific article published on 5 January 2018

Isolation of Intact Mitochondria from the Model Plant Species Arabidopsis thaliana and Oryza sativa

scientific article

Isolation of a novel soybean gene encoding a mitochondrial ATP synthase subunit.

scientific article published in September 1994

Isolation of tissues and preservation of RNA from intact, germinated barley grain

scientific article published on 16 May 2017

LETM proteins play a role in the accumulation of mitochondrially encoded proteins in Arabidopsis thaliana and AtLETM2 displays parent of origin effects

scientific article

Ligand recognition by the TPR domain of the import factor Toc64 from Arabidopsis thaliana

scientific article

MPIC: a mitochondrial protein import components database for plant and non-plant species.

scientific article

Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process

scientific article

Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles

scientific article published on April 2015

Mitochondrial Defects Confer Tolerance against Cellulose Deficiency.

scientific article published on 19 August 2016

Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases

scientific article

Mitochondrial biogenesis in plants during seed germination

scientific article published on 13 April 2014

Mitochondrial protein import in plants. Signals, sorting, targeting, processing and regulation

scientific article published on 01 September 1998

Mitochondrial signalling is critical for acclimation and adaptation to flooding in Arabidopsis thaliana

scientific article published on 16 February 2020

Mitochondrial targeting of the Arabidopsis F1-ATPase γ-subunit via multiple compensatory and synergistic presequence motifs

scientific article published on 18 December 2012

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

scientific article published on 11 April 2006

Molecular distinction between alternative oxidase from monocots and dicots

scientific article

Molecular interaction between PHO2 and GIGANTEA reveals a new crosstalk between flowering time and phosphate homeostasis in Oryza sativa

scientific article published on 24 March 2017

Multiple lines of evidence localize signaling, morphology, and lipid biosynthesis machinery to the mitochondrial outer membrane of Arabidopsis.

scientific article

Mutation in xyloglucan 6-xylosytransferase results in abnormal root hair development in Oryza sativa.

scientific article

Next generation sequencing and de novo transcriptomics to study gene evolution

scientific article

Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria

scientific article published on 21 November 2006

Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination.

scientific article published on 16 February 2012

Nutrient stress-induced chromatin changes in plants

scientific article

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts

scientific article published on 16 September 2013

Organic acid activation of the alterNatlve oxidase of plant mitochondria

article

OsNLA1, a RING-type ubiquitin ligase, maintains phosphate homeostasis in Oryza sativa via degradation of phosphate transporters

scientific article published on 23 February 2017

Overexpression ofOsPAP10a, A Root-Associated Acid Phosphatase, Increased Extracellular Organic Phosphorus Utilization in Rice

article

Phage-type RNA polymerase RPOTmp performs gene-specific transcription in mitochondria of Arabidopsis thaliana.

scientific article

Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis.

scientific article

Plant-Specific Preprotein and Amino Acid Transporter Proteins Are Required for tRNA Import into Mitochondria

scientific article published on 27 October 2016

Processing of precursor proteins by plant mitochondria

scientific article published on 01 June 1990

Protein import into mitochondria: origins and functions today (review).

scientific article

Protein import into plant mitochondria: precursor proteins differ in ATP and membrane potential requirements.

scientific article published in February 2001

Protein import into plant mitochondria: signals, machinery, processing, and regulation

scientific article

Protein phosphorylation stimulates the rate of malate uptake across the peribacteroid membrane of soybean nodules

scientific article

Protein transport in organelles: Dual targeting of proteins to mitochondria and chloroplasts

scientific article published on March 2009

Proteomic and Carbonylation Profile Analysis at the Critical Node of Seed Ageing in Oryza sativa

scientific article published on 17 January 2017

Quantification of the common deletion in human testicular mitochondrial DNA by competitive PCR assay using a chimaeric competitor

scientific article published on 01 March 2001

REDOX regulation of mitochondrial function in plants

scientific article published on 24 March 2011

RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album

scientific article

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin

scientific article

Random mutagenesis of human estrogen receptor ligand binding domain identifies mutations that decrease sensitivity to estradiol and increase sensitivity to a diphenol indene-ol compound: Basis for a regulatable expression system ⬇️

scientific article published on February 1, 1998

Regulation of alternative oxidase gene expression in soybean

scientific article published in November 2002

Respiratory gene expression in soybean cotyledons during post-germinative development

scientific article published in March 2003

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis

scientific article

Rice SPX-Major Facility Superfamily3, a Vacuolar Phosphate Efflux Transporter, Is Involved in Maintaining Phosphate Homeostasis in Rice.

scientific article

Root Cell-Specific Regulators of Phosphate-Dependent Growth

scientific article published on 2 May 2017

SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis

scientific article published on 01 July 2019

Sequencing of a soybean alternative oxidase cDNA clone.

scientific article published in December 1993

Signals required for the import and processing of the alternative oxidase into mitochondria

scientific article published on 01 January 1999

Spatially resolved transcriptomic analysis of the germinating barley grain

scientific article published in 2023

Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery

scientific article

Specificity of leaf mitochondrial and chloroplast processing systems for nuclear-encoded precursor proteins

scientific article published on 01 February 1991

Stepwise Evolution of a Buried Inhibitor Peptide over 45 My.

scientific article published on 8 March 2017

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

scientific article

Stress responsive mitochondrial proteins in Arabidopsis thaliana

scientific article published on 16 March 2018

Studies on the import and processing of the alternative oxidase precursor by isolated soybean mitochondria

scientific article published on 01 February 1995

Subcomplexes of ancestral respiratory complex I subunits rapidly turn over in vivo as productive assembly intermediates in Arabidopsis

scientific article

Sulphur dioxide evokes a large scale reprogramming of the grape berry transcriptome associated with oxidative signalling and biotic defence responses

scientific article published on 18 July 2011

Superoxide stimulates a proton leak in potato mitochondria that is related to the activity of uncoupling protein

scientific article published on 2 April 2003

TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana

scientific article published on 23 December 2010

Temporal regulation of in vitro import of precursor proteins into tobacco mitochondria

scientific article published on 01 September 1997

Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination

scientific article published on 03 December 2019

The Design and Structure of Outer Membrane Receptors from Peroxisomes, Mitochondria, and Chloroplasts

scientific article

The Expression of Alternative Oxidase and Uncoupling Protein during Fruit Ripening in Mango

scientific article published on 01 August 2001

The N-terminal cleavable extension of plant carrier proteins is responsible for efficient insertion into the inner mitochondrial membrane

scientific article published in August 2005

The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content

scientific article published on 23 February 2018

The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana.

scientific article

The Soybean Sugar Transporter GmSWEET15 Mediates Sucrose Export from Endosperm to Early Embryo

scientific article published on 20 June 2019

The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a.

scientific article published on 6 February 2017

The dual targeting ability of type II NAD(P)H dehydrogenases arose early in land plant evolution

scientific article

The function of the <i>Medicago truncatula</i> ZIP transporter MtZIP14 is linked to arbuscular mycorrhizal fungal colonization

scientific article published in 2023

The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis

scientific article

The mitochondrial outer membrane AAA ATPase AtOM66 affects cell death and pathogen resistance in Arabidopsis thaliana

scientific article published on November 2014

The mitochondrial protein import component, TRANSLOCASE OF THE INNER MEMBRANE17-1, plays a role in defining the timing of germination in Arabidopsis.

scientific article published on 24 September 2014

The outer mitochondrial membrane in higher plants

scientific article published on 02 January 2013

The plant mitochondrial protein import apparatus - the differences make it interesting

scientific article published on 28 September 2013

Tissue-specific expression of the alternative oxidase in soybean and siratro.

scientific article published in June 1992

Tom22', an 8-kDa trans-site receptor in plants and protozoans, is a conserved feature of the TOM complex that appeared early in the evolution of eukaryotes

scientific article published on 21 May 2004

Torsion-induced injury in rat testes does not affect mitochondrial respiration or the accumulation of mitochondrial mutations

scientific article published on 01 December 2000

Towards an analysis of the rice mitochondrial proteome

scientific article published on May 2003

Two h-Type Thioredoxins Interact with the E2 Ubiquitin Conjugase PHO2 to Fine-Tune Phosphate Homeostasis in Rice.

scientific article published on 28 November 2016

Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana

scientific article published on 12 August 2008

Unique components of the plant mitochondrial protein import apparatus

scientific article

What happens to plant mitochondria under low oxygen? An omics review of the responses to low oxygen and reoxygenation

scientific article published on 11 May 2014

Widespread dual targeting of proteins in land plants: When, where, how and why ⬇️

scientific article published on May 31, 2013

Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria.

scientific article published in June 2002

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