4.7 Article

Spatial proteomics reveals subcellular reorganization in human keratinocytes exposed to UVA light

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

Proper imputation of missing values in proteomics datasets for differential expression analysis

Mingyi Liu et al.

Summary: Label-free shotgun proteomics is an important tool in biomedical research, but the DDA datasets often contain missing values that hinder proper analysis. This study investigated the composition of missing values in various tissue/sample types and compared the impact of different imputation methods on differential expression analysis of proteins, providing recommendations for proteomic data.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Cell Biology

NIX initiates mitochondrial fragmentation via DRP1 to drive epidermal differentiation

Cory L. Simpson et al.

Summary: This study reveals that regulated breakdown of mitochondria is critical for epidermal development, with keratinocytes in the upper layers initiating mitochondrial fragmentation, depolarization, and acidification. The mitophagy receptor NIX and DRP1 play essential roles in driving epidermal morphogenesis by promoting mitochondrial degradation in the terminal differentiation of keratinocytes.

CELL REPORTS (2021)

Article Biochemical Research Methods

A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Data Sets

Kruttika Dabke et al.

Summary: The study evaluated different imputation methods on clinical data sets and found that the suitability of imputation methods depends on the overall structure of the data set. Imputation at the fragment level improved accuracy and the number of proteins quantified. This study provides an example of an analytical framework that may assist in identifying appropriate imputation strategies for the analysis of proteins.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Biochemistry & Molecular Biology

Whole-exome sequencing reveals the impact of UVA light mutagenesis in xeroderma pigmentosum variant human cells

Natalia Cestari Moreno et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biochemistry & Molecular Biology

Reciprocal Regulation of Mitochondrial Fission and Fusion

Rasha Sabouny et al.

TRENDS IN BIOCHEMICAL SCIENCES (2020)

Article Biochemical Research Methods

TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets

Michelle A. Kennedy et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Review Genetics & Heredity

DNA Damage Response and Metabolic Reprogramming in Health and Disease

Ourania Chatzidoukaki et al.

TRENDS IN GENETICS (2020)

Article Biochemistry & Molecular Biology

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Mitochondrial morphology regulates organellar Ca2+ uptake and changes cellular Ca2+ homeostasis

Alicia J. Kowaltowski et al.

FASEB JOURNAL (2019)

Review Cell Biology

The Good and the Bad of Mitochondrial Breakups

Hans-Georg Sprenger et al.

TRENDS IN CELL BIOLOGY (2019)

Review Cell Biology

Spatial proteomics: a powerful discovery tool for cell biology

Emma Lundberg et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Multidisciplinary Sciences

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

Aikaterini Geladaki et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

Quantifying compartment-associated variations of protein abundance in proteomics data

Luca Parca et al.

MOLECULAR SYSTEMS BIOLOGY (2018)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2017)

Review Biochemistry & Molecular Biology

Sunlight damage to cellular DNA: Focus on oxidatively generated lesions

Andre Passaglia Schuch et al.

FREE RADICAL BIOLOGY AND MEDICINE (2017)

Editorial Material Multidisciplinary Sciences

The Human Cell Atlas: from vision to reality

Orit Rozenblatt-Rosen et al.

NATURE (2017)

Article Biochemical Research Methods

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

Claire M. Mulvey et al.

NATURE PROTOCOLS (2017)

Article Multidisciplinary Sciences

A subcellular map of the human proteome

Peter J. Thul et al.

SCIENCE (2017)

Article Cell Biology

Multilayered Reprogramming in Response to Persistent DNA Damage in C. elegans

Diletta Edifizi et al.

CELL REPORTS (2017)

Article Biochemical Research Methods

The Perseus computational platform for comprehensive analysis of (prote)omics data

Stefka Tyanova et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks

Chunshui Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Cell Biology

High-Content Screening for Quantitative Cell Biology

Mojca Mattiazzi Usaj et al.

TRENDS IN CELL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response

Andrew E. H. Elia et al.

MOLECULAR CELL (2015)

Review Cell Biology

Multidimensional proteomics for cell biology

Mark Larance et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Multidisciplinary Sciences

Chemiexcitation of melanin derivatives induces DNA photoproducts long after UV exposure

Sanjay Premi et al.

SCIENCE (2015)

Article Biochemical Research Methods

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

Laurent Gatto et al.

BIOINFORMATICS (2014)

Review Dermatology

UV Signaling Pathways within the Skin

Hongxiang Chen et al.

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2014)

Article Biochemical Research Methods

A Foundation for Reliable Spatial Proteomics Data Analysis

Laurent Gatto et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Biochemical Research Methods

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

Juergen Cox et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Review Cell Biology

The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

Michal Breker et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Review Biochemistry & Molecular Biology

The Interplay Between Mitochondrial Dynamics and Mitophagy

Gilad Twig et al.

ANTIOXIDANTS & REDOX SIGNALING (2011)

Article Biochemical Research Methods

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

Juergen Cox et al.

JOURNAL OF PROTEOME RESEARCH (2011)

Article Multidisciplinary Sciences

Stochastic fate of p53-mutant epidermal progenitor cells is tilted toward proliferation by UV B during preneoplasia

Allon M. Klein et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

SLP-2 is required for stress-induced mitochondrial hyperfusion

Daniel Tondera et al.

EMBO JOURNAL (2009)

News Item Oncology

A review of human carcinogens - Part D: radiation

Fatiha El Ghissassi et al.

LANCET ONCOLOGY (2009)

Article Biochemistry & Molecular Biology

In CK2 inactivated cells the cyclin dependent kinase inhibitor Sic1 is involved in cell-cycle arrest before the onset of S phase

Farida Tripodi et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)

Article Biochemistry & Molecular Biology

A mammalian organelle map by protein correlation profiling

LJ Foster et al.

Article Dermatology

UVA-induced modification of catalase charge properties in the epidermis is correlated with the skin phototype

Vittoria Maresca et al.

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2006)

Review Biochemistry & Molecular Biology

Endogenous UVA-photosensitizers: mediators of skin photodamage and novel targets for skin photoprotection

GT Wondrak et al.

PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES (2006)

Article Dermatology

Expression profiling of human keratinocyte response to ultraviolet A: Implications in apoptosis

YY He et al.

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2004)

Article Biochemistry & Molecular Biology

Phosphorylation of XPB helicase regulates TFIIH nucleotide excision repair activity

F Coin et al.

EMBO JOURNAL (2004)

Article Dermatology

Induction of the photoaging-associated mitochondrial common deletion in vivo in normal human skin

M Berneburg et al.

JOURNAL OF INVESTIGATIVE DERMATOLOGY (2004)

Article Multidisciplinary Sciences

Proteomic characterization of the human centrosome by protein correlation profiling

JS Andersen et al.

NATURE (2003)

Article Biochemistry & Molecular Biology

UV-induced DNA damage, repair, mutations and oncogenic pathways in skin cancer

FR de Gruijl et al.

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY (2001)

Article Biochemistry & Molecular Biology

UV-A irradiation induces a decrease in the mitochondrial respiratory activity of human NCTC 2544 keratinocytes

M Djavaheri-Mergny et al.

FREE RADICAL RESEARCH (2001)