Search filters

List of works by Kathryn Lilley

<i>Drosophila</i> nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins

scientific article published on 16 May 2022

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

scientific article published on 27 November 2018

A Bayesian semi-parametric model for thermal proteome profiling

scientific article published on 29 June 2021

A Bioconductor workflow for processing and analysing spatial proteomics data

scientific article published on 28 December 2016

A Bioconductor workflow for the Bayesian analysis of spatial proteomics

scientific article published on 11 April 2019

A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions

scientific article published on 08 October 2020

A Protocol to Map the Spatial Proteome Using HyperLOPIT in <i>Saccharomyces cerevisiae</i>

publication published on 20 July 2019

A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana.

scientific article

A combined metabolomic and proteomic investigation of the effects of a failure to express dystrophin in the mouse heart

scientific article published on 3 April 2008

A direct role for SNX9 in the biogenesis of filopodia

scientific article published on 01 April 2020

A draft map of the mouse pluripotent stem cell spatial proteome

scientific article published on 12 January 2016

A foundation for reliable spatial proteomics data analysis.

scientific article

A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis

scientific article published on 17 December 2012

A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells

scientific article published on 01 March 2019

A proteomics approach to membrane trafficking

scientific article published on August 2008

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

scientific article published on 09 November 2020

A subcellular map of the human proteome

scientific article

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

scientific article

A time-resolved proteomic and prognostic map of COVID-19

scientific article published on 14 June 2021

Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS).

scientific article published on 16 June 2014

Addressing accuracy and precision issues in iTRAQ quantitation

scientific article published on 10 April 2010

An open invitation to the Understudied Proteins Initiative

scientific article published on 9 May 2022

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches

scientific article

Analysis of Quality-Related Parameters in Mature Kernels of Polygalacturonase Inhibiting Protein (PGIP) Transgenic Bread Wheat Infected with Fusarium graminearum

scientific article published on 9 April 2015

Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts

scientific article published on 23 December 2004

Analysis of temperature-mediated changes in the wine yeast Saccharomyces bayanus var uvarum. An oenological study of how the protein content influences wine quality

scientific article published in December 2015

Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library

scientific article

Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination

scientific article

Application of partial least squares discriminant analysis to two-dimensional difference gel studies in expression proteomics

article

Assessing sub-cellular resolution in spatial proteomics experiments

Assessing sub-cellular resolution in spatial proteomics experiments

Author Correction: Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)

scientific article published on 01 June 2019

Big results from small samples: evaluation of amplification protocols for gene expression profiling.

scientific article published in July 2007

Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions

scientific article published on 22 January 2020

Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I.

scientific article

Challenges for proteomics core facilities

scientific article

Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms

scientific article published on 11 April 2019

Changes in the oligodendrocyte progenitor cell proteome with ageing

scientific article published on 20 May 2020

Chapter 19 Measuring redox changes to mitochondrial protein thiols with redox difference gel electrophoresis (redox-DIGE).

scientific article published in January 2009

Characterisation of protein isoforms encoded by the Drosophila Glycogen Synthase Kinase 3 gene shaggy

scientific article published on 06 August 2020

Characterization of the necrotic protein that regulates the Toll-mediated immune response in Drosophila

scientific article published on 31 October 2002

Circadian orchestration of the hepatic proteome

scientific article published in June 2006

Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

scientific article published on 03 May 2020

Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation.

scientific article published on 30 January 2018

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

scientific article published in Nature Communications

Comparative gel-based phosphoproteomics in response to signaling molecules.

scientific article published in January 2013

Comparative proteomics of clathrin-coated vesicles

scientific article

Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics

article

Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules

scientific article published on 22 May 2019

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

scientific article published on 03 January 2019

Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds

scientific article published on 01 January 2005

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

scientific article published on 25 November 2019

DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.

scientific article published on 25 March 2004

Deciphering thylakoid sub-compartments using a mass spectrometry-based approach.

scientific article

Design and analysis issues in quantitative proteomics studies

scientific article published on September 2007

Detection of reactive oxygen species-sensitive thiol proteins by redox difference gel electrophoresis: implications for mitochondrial redox signaling

scientific article published on 24 May 2007

Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics

scientific article published on 01 January 2008

Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis

scientific article published in May 2004

Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification

scientific article published on 01 January 2014

Differential Interactome and Innate Immune Response Activation of Two Structurally Distinct Misfolded Protein Oligomers

scientific article published on 02 August 2019

Drosophila Ionotropic Receptor 25a mediates circadian clock resetting by temperature.

scientific article published on 18 November 2015

Drosophila Larp associates with poly(A)-binding protein and is required for male fertility and syncytial embryo development.

scientific article published on 22 July 2009

Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components

scientific article published on 01 January 2019

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells

scientific article published on 8 June 2015

Dynamic regulation of the COP9 signalosome in response to DNA damage

scientific article

Early Responses to Severe Drought Stress in the Cell Suspension Culture Proteome

article

Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies

scientific article

Efficient recovery of the RNA-bound proteome and protein-bound transcriptome using phase separation (OOPS)

scientific article published on 10 July 2020

Enabling technologies for yeast proteome analysis

scientific article published on January 2011

Erratum to: Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination

scientific article published on 9 May 2016

Erratum to: Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination.

scientific article published on 8 May 2017

Ethylene Receptors, CTRs and EIN2 Target Protein Identification and Quantification Through Parallel Reaction Monitoring During Tomato Fruit Ripening

scientific article published on 08 November 2018

Experimental and Statistical Considerations to Avoid False Conclusions in Proteomics Studies Using Differential In-gel Electrophoresis

scientific article published on 17 May 2007

Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage

scientific article

FlyMine: an integrated database for Drosophila and Anopheles genomics

scientific article published on January 2007

Focus on Quantitative Proteomics

article

Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors

scientific article

GARNet, the Genomic Arabidopsis Resource Network

scientific article

Gel-Based Proteomics Approach to the Study of Metabolic Changes in Pear Tissue during Storage

scientific article published on 01 August 2009

Genomic tagging reveals a random association of endogenous PtdIns5P 4-kinases IIalpha and IIbeta and a partial nuclear localization of the IIalpha isoform

scientific article

Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus

scientific article published on September 2017

Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

scientific article published on 25 November 2020

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

scientific article

Glucocorticoid signaling synchronizes the liver circadian transcriptome

scientific article published on 01 June 2007

Growth control of the eukaryote cell: a systems biology study in yeast ⬇️

scientific article (publication date: 2007)

Guidelines for reporting the use of gel electrophoresis in proteomics.

scientific article

Guidelines for reporting the use of mass spectrometry in proteomics.

scientific article

Human urinary exosomes as innate immune effectors

scientific article

Identification and Quantitation of Signal Molecule-Dependent Protein Phosphorylation ⬇️

scientific article published on January 1, 2013

Identification of S-nitrosated mitochondrial proteins by S-nitrosothiol difference in gel electrophoresis (SNO-DIGE): implications for the regulation of mitochondrial function by reversible S-nitrosation

scientific journal article

Identification of clock genes using difference gel electrophoresis

scientific article

Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis

scientific article

Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks

scientific article

Identification of the cis‑molecular neighbours of the immune checkpoint protein B7‑H4 in the breast cancer cell‑line SK‑BR‑3 by proteomic proximity labelling

scientific article published on 03 April 2020

Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue

scientific article published on 17 January 2014

Impact of replicate types on proteomic expression analysis

scientific article published in September 2005

Improved sub‐cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions ⬇️

scientific article published on December 1, 2010

Improving qualitative and quantitative performance for MS(E)-based label-free proteomics

scientific article published on 17 April 2013

In Depth Exploration of the Alternative Proteome of Drosophila melanogaster

scientific article published on 01 January 2022

In vivo analyses of the roles of essential Omp85-related proteins in the chloroplast outer envelope membrane

scientific article published on 14 July 2011

In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry ⬇️

scientific article

In-depth characterization of the tomato fruit pericarp proteome.

scientific article published on 13 December 2016

Interaction between Anillin and RacGAP50C connects the actomyosin contractile ring with spindle microtubules at the cell division site

scientific article

Investigating sample pooling strategies for DIGE experiments to address biological variability

scientific article

Isolation and preparation of chloroplasts from Arabidopsis thaliana plants

scientific article published in January 2008

Ketamine's Effects on the Glutamatergic and GABAergic Systems: A Proteomics and Metabolomics Study in Mice

scientific article published on 15 November 2018

Ketamine's antidepressant effect is mediated by energy metabolism and antioxidant defense system

scientific article

LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies

scientific article

LOPIT-DC: A simpler approach to high-resolution spatial proteomics

Label-free protein quantification for plant Golgi protein localization and abundance.

scientific article published on 13 August 2014

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

scientific article

MRMaid 2.0: mining PRIDE for evidence-based SRM transitions

scientific article

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions

scientific article

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

scientific article

Mapping organelle proteins and protein complexes in Drosophila melanogaster

scientific article

Mapping the Arabidopsis organelle proteome

scholarly article

Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT

scientific article published on 01 January 2019

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.

scientific article

Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes

scientific article published on 01 August 2005

Molecular analysis of core kinetochore composition and assembly in Drosophila melanogaster

scientific article

Moving Profiling Spatial Proteomics Beyond Discrete Classification

scientific article published on 17 June 2020

Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.

scientific article

Multiple protein phosphatases are required for mitosis in Drosophila.

scientific article published in February 2007

Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency

scientific article published on 12 June 2018

New insights into the DT40 B cell receptor cluster using a proteomic proximity labeling assay

scientific article

Nutrient control of eukaryote cell growth: a systems biology study in yeast

scientific article

Organelle proteomics experimental designs and analysis

scientific article

PEDRo: a database for storing, searching and disseminating experimental proteomics data

scientific article

Palmitoylation in plants: new insights through proteomics

scientific article published on 5 June 2013

Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

scientific article published on 25 January 2021

Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1.

scientific article published on 3 August 2016

Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling

scientific article published on 16 October 2012

Plant endoplasmin supports the protein secretory pathway and has a role in proliferating tissues

scientific article published on 19 October 2006

Prior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments

scientific article published on 09 March 2022

Protein Neighbors and Proximity Proteomics

scientific article

Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism

scientific article published on 02 October 2019

Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation

scientific article published on 01 February 2022

Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE).

scientific article

Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock

scientific article published on 12 November 2009

Proteomic approaches to the characterization of protein thiol modification ⬇️

scientific article published on December 2, 2010

Proteomic comparison of various hepatic cell cultures for preclinical safety pharmacology.

scientific article published on 4 April 2018

Proteomic complex detection using sedimentation

scientific article published on 01 March 2007

Proteomic complex detection using sedimentation (ProCoDeS): screening for proteins in stable complexes and their candidate interaction partners

scientific article published on August 2010

Proteomic responses of HepG2 cell monolayers and 3D spheroids to selected hepatotoxins

article

Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics

scientific article published on 24 August 2012

Quantification and identification of mitochondrial proteins containing vicinal dithiols

scientific article published on 15 September 2010

Quantitative proteomic approach to study subcellular localization of membrane proteins

scientific article published on 01 January 2006

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

scientific article

Recruitment of Polo kinase to the spindle midzone during cytokinesis requires the Feo/Klp3A complex

scientific article (publication date: 2007)

SETH1 and SETH2, two components of the glycosylphosphatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in Arabidopsis

scientific article published on 11 December 2003

SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture

scientific article

SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis

scientific article

SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos

scientific article

Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization

scientific article published on 02 July 2019

Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis

scientific article published on October 2008

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

scientific article published on 25 November 2020

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

scientific article published on 01 October 2021

Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum

scientific article published on 18 September 2017

Stat3 mediated alterations in lysosomal membrane protein composition

scientific article published on 17 January 2018

Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins

scientific article published on 5 January 2013

Sub-cellular localization of membrane proteins

scientific article

Subcellular proteomics

scientific article published on 29 April 2021

The ABRF MARG microarray survey 2005: taking the pulse of the microarray field

scientific article published on April 2006

The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins.

scientific article

The Drosophila melanogaster sperm proteome-II (DmSP-II) ⬇️

scientific article published on September 15, 2010

The RNA-binding protein repertoire of Arabidopsis thaliana

scientific article published on 11 July 2016

The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

article by Jakob Vowinckel et al published 2013 in F1000Research

The chicken B-cell line DT40 proteome, beadome and interactomes

scientific article published on 13 January 2015

The dominant cold-sensitive Out-cold mutants of Drosophila melanogaster have novel missense mutations in the voltage-gated sodium channel gene paralytic

scientific article published on 24 August 2008

The metabolic background is a global player in Saccharomyces gene expression epistasis

scientific article published on February 2016

The organelle proteome of the DT40 lymphocyte cell line.

scientific article

The subcellular organisation of Saccharomyces cerevisiae

scientific article published on 29 November 2018

Time, space, and disorder in the expanding proteome universe

scientific article

Toward a comprehensive map of the effectors of rab GTPases

scientific article

Towards reproducible MSMS data preprocessing, quality control and quantification

Tracking the embryonic stem cell transition from ground state pluripotency

scientific article

Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae

scientific article published on 01 March 2019

Two-dimensional differential in gel electrophoresis (2D-DIGE) analysis of grape berry proteome during postharvest withering

scientific article published in December 2010

Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation

scientific article

Ubiquitination of alpha-synuclein in Lewy bodies is a pathological event not associated with impairment of proteasome function

scientific article published on 15 August 2003

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

scientific article published on 02 June 2020

Understudied proteins: opportunities and challenges for functional proteomics

scientific article published on 9 May 2022

Uromodulin exclusion list improves urinary exosomal protein identification ⬇️

scientific article published on December 1, 2011

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

scientific article

hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α1-antitrypsin deficiency.

scientific article published on 5 June 2018

i-Tracker: for quantitative proteomics using iTRAQ.

scientific article

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

α-Klotho Expression in Human Tissues.

scientific article

Paulina is supported by:

About Paulina

Help