Publications related to Proteome

Development of tools and methods for protein identification: From single molecules to in vivo applications

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Comprehensive proteomic analysis of JC polyomavirus-infected human astrocytes and their extracellular vesicles

Alexey Sapozhnik, Samuel Jones

JC polyomavirus (JCPyV) is an opportunistic virus that remains in a latent state in the kidneys and lymphoid organs of more than half of the human adult population. In rare cases of severe immune suppression, the virus is able to establish a lytic infectio ...

Amer Soc Microbiology2023

Proteomics reveals unique plasma signatures in constitutional thinness

Loïc Dayon, Jörg Hager, Nele Gheldof

Purpose Studying the plasma proteome of control versus constitutionally thin (CT) individuals, exposed to overfeeding, may give insights into weight-gain management, providing relevant information to the clinical entity of weight-gain resistant CT, and dis ...

WILEY-V C H VERLAG GMBH2022

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples

Loïc Dayon

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

ELSEVIER SCI LTD2022

Dual proteomics of Drosophila melanogaster hemolymph infected with the heritable endosymbiont Spiroplasma poulsonii

Bruno Lemaitre, Samuel Rommelaere, Fanny Schüpfer, Florent François Masson, Alice Marra

Insects are frequently infected with heritable bacterial endosymbionts. Endosymbionts have a dramatic impact on their host physiology and evolution. Their tissue distribution is variable with some species being housed intracellularly, some extracellularly ...

2021

DBnorm as an R package for the comparison and selection of appropriate statistical methods for batch effect correction in metabolomic studies

Nicolas Jean Philippe Guex, Murielle Bochud, Cristian Carmeli, Aurélien Thomas, Tiziana Caputo

As a powerful phenotyping technology, metabolomics provides new opportunities in biomarker discovery through metabolome-wide association studies (MWAS) and the identification of metabolites having a regulatory effect in various biological processes. While ...

Nature Research2021

Single-cell lipidomics reveals a role for cell-to-cell sphingolipid heterogeneity in fibroblast activation

Laura Capolupo

Cell-to-cell variability plays a key role in tissue patterning by setting initial asymmetry that primes cell fate decisions. Fluctuations in the activity of regulatory molecules can commit individual cells to divergent differentiation pathways, and cell-to ...

EPFL2021

The functional proteome landscape of Escherichia coli

Camille Véronique Bernadette Goemans

Recent developments in high-throughput reverse genetics1,2 have revolutionized our ability to map gene function and interactions3,4,5,6. The power of these approaches depends on their ability to identify functionally associated genes, which elicit similar ...

2020

Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry

Loïc Dayon

Cerebrospinal fluid (CSF) is a biofluid in direct contact with the brain and as such constitutes a sample of choice in neu-rological disorder research, including neurodegenerative dis-eases such as Alzheimer or Parkinson. Human CSF has still been less stud ...

2020

Progress and pitfalls of using isobaric mass tags for proteome profiling

Loïc Dayon

Introduction: Quantitative proteomics using mass spectrometry is performed via label-free or label-based approaches. Labeling strategies rely on the incorporation of stable heavy isotopes by metabolic, enzymatic, or chemical routes. Isobaric labeling uses ...

TAYLOR & FRANCIS LTD2020

Development of chemical biology tools to reveal the function and organization of the silenced chromatin state

Nora Guidotti

Effector proteins are recruited to chromatin via transient interactions between their reader domains and histone post-translational modification (PTM) patterns. These interactions form signaling pathways that control gene expression or repression and which ...

EPFL2020

Mitochondrial ph probe

Anders Meibom, Matthias Lütolf, Gennady Nikitin

The present invention relates to dual fluorophore ratiometric mitochondrial pH probes, their uses and their manufacture. ...

2019

Functional characterization of 3D protein structures informed by human genetic diversity

Amalio Telenti, Istvan Bartha, Julia di Iulio

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homolog ...

National Academy of Sciences2019

Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

Jacques Fellay, Nimisha Chaturvedi

Genetic polymorphism in the interferon lambda (IFN-lambda) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and response to interferon-based treatment. Here, we evaluate associations between IFN-l polymorphism and HCV va ...

2019

Weighing up the Selenocysteome Uncovers New Sec-rets

Yimon Aye, Jesse Poganik

Challenging the paradigm of SECIS-dependent selenoprotein translation, in this issue of Cell Chemical Biology Guo et al. (2018) introduce a new selenoprotein profiling platform with which they identify novel selenoproteins apparently lacking SECIS. With in ...

CELL PRESS2018

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population

Johan Auwerx, Jun Yong Kim, Dongryeol Ryu, Evan Graehl Williams, Pooja Jha, Jiayi Lan, Ruedi Aebersold, Moaraj Hasan

We have used SWATH mass spectrometry to quantify 3648 proteins across 76 proteomes collected from genetically diverse BXD mouse strains in two fractions (mitochondria and total cell) from five tissues: liver, quadriceps, heart, brain, and brown adipose (BA ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2018

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

Bart Deplancke, Jacques Rougemont

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing geneand transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification o ...

Oxford University Press2017

Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies

Kristina Pan Woodruff

With the advent of high-throughput and genome-wide screening initiatives, there is a need for improved methods for cell-based assays. Current approaches require expensive equipment, rely on large-scale culturing formats not suited for small or rare sample ...

EPFL2017

Expression proteomics study to determine metallodrug targets and optimal drug combinations

Paul Joseph Dyson, Kai Johnsson, David Hacker, Claire Samantha Allardyce

The emerging technique termed functional identification of target by expression proteomics (FITExP) has been shown to identify the key protein targets of anti-cancer drugs. Here, we use this approach to elucidate the proteins involved in the mechanism of a ...

Nature Research2017