Publications related to Comprehensive and Scalable Highly Automated MS-Based Proteomic Workflow for Clinical Biomarker Discovery in Human Plasma

Related publications (30)

Iron-carbohydrate complexes treating iron anaemia: Understanding the nano-structure and interactions with proteins through orthogonal characterisation

Antonia Neels, Marianne Liebi, Tiberiu Totu

Intravenous (IV) iron-carbohydrate complexes are widely used nanoparticles (NPs) to treat iron deficiency anaemia, often associated with medical conditions such as chronic kidney disease, heart failure and various inflammatory conditions. Even though a ple ...

Elsevier2024

Orchestrating chromosome conformation capture analysis with Bioconductor

Cyril Matthey-Doret

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Data and Workflow to: Three-dimensional buoyant hydraulic fractures: finite volume release (Möri and Lecampion, (2023))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fractures: finite volume release" by Möri and Lecampion, (2023). ...

Zenodo2023

Building a Knowledge Graph of Chinese Kung Fu Masters From Heterogeneous Bilingual Data

Lin Yuan, Yumeng Hou, Lin Yuan

Various endeavours into semantic web technologies and ontology engineering have been made within the organisation of cultural data, facilitating public access to digital assets. Although models for conceptualising objects have reached a certain level of ma ...

2023

A study of the K^(+) → π^(0)e^(+)νγ decay

Alessandro Mapelli, Alina Kleimenova, Radoslav Marchevski

A sample of 1.3 x 10^(5) K^(+) → π^(0)e^(+)νγ candidates with less than 1% background was collected by the NA62 experiment at the CERN SPS in 2017-2018. Branching fraction measurements are obtained at percent relative precision in three restricted kinemati ...

Springer Nature2023

Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows

Giovanni Pizzi, Antimo Marrazzo, Junfeng Qiao

The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and implementations ...

NATURE PORTFOLIO2023

A Robust Framework for Generating Adsorption Isotherms to Screen Materials for Carbon Capture

Berend Smit, Seyedmohamad Moosavi, Elias Moubarak

To rank the performanceof materials for a given carbon captureprocess, we rely on pure component isotherms from which we predictthe mixture isotherms. For screening a large number of materials,we also increasingly rely on isotherms predicted from molecular ...

AMER CHEMICAL SOC2023

Combining ion mobility spectrometry and cryogenic ion spectroscopy with enzymatic digestion/synthesis for the study of N-linked glycans

Irina Märki

Glycans play an essential role in numerous physiological and pathological processes of living organisms. Despite their significant biological relevance, glycobiology remains one of the least explored fields of biochemistry. The intrinsic isomeric complexit ...

EPFL2023

Robust optimization of control parameters for WEC arrays using stochastic methods

Tommaso Vanzan

This work presents a new computational optimization framework for the robust control of parks of Wave Energy Converters (WEC) in irregular waves. The power of WEC parks is maximized with respect to the individual control damping and stiffness coefficients ...

Journal of Computational Physics2023

AiiDA-defects: an automated and fully reproducible workflow for the complete characterization of defect chemistry in functional materials

Nicola Marzari, Sokseiha Muy, Conrad Johnston

Functional materials that enable many technological applications in our everyday lives owe their unique properties to defects that are carefully engineered and incorporated into these materials during processing. However, optimizing and characterizing thes ...

IOP Publishing Ltd2023

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Maria del Carmen Sandi Perez

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

PERGAMON-ELSEVIER SCIENCE LTD2023

New Approach for the Identification of Isobaric and Isomeric Metabolites

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Ali H Abikhodr

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often require ...

2023

Advancing Glycan Analysis: Cryogenic Ion Spectroscopy for Database-Driven Identification

Ali H Abikhodr

Glycans play a pivotal role in both physiological processes; however, the field of glycobiology remains relatively understudied within biochemistry. The intricate complexity of glycans, coupled with their abundance of isomeric forms, presents formidable ch ...

EPFL2023

Rapid low-cost hyperspectral imaging system for quantitative assessment of infantile hemangioma

Viktor Vorobev

Hemangioma, the predominant benign tumor occurring in infancy, exhibits a wide range of prognoses and associated outcomes. The accurate determination of prognosis through noninvasive imaging modalities holds essential importance in enabling effective perso ...

Wiley-V C H Verlag Gmbh2023

Modeling tumor size dynamics based on real-world electronic health records and image data in advanced melanoma patients receiving immunotherapy

Federico Amato

The development of immune checkpoint inhibitors (ICIs) has revolutionized cancer therapy but only a fraction of patients benefits from this therapy. Model-informed drug development can be used to assess prognostic and predictive clinical factors or biomark ...

2023

Performance investigation of cameras using HDR sensors for daylight glare evaluations

Jan Wienold, Geraldine Cai Ting Quek, Dong Hyun Kim

This study presents a novel framework for evaluating the luminance measurement capabilities of High Dynamic Range (HDR) sensor cameras in indoor glare conditions. Results indicate that the practical usage range of the CSEM VIP camera is significantly lower ...

International Commission on Illumination2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

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

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

Data and Workflow to: Three-dimensional buoyant hydraulic fracture growth: constant release from a point source (Möri and Lecampion, (2022))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fracture growth: constant release from a point source" by Möri and Lecampion, (2022 ...

2022