Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions

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Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints

Pablo Rivera Fuentes, Salome Riccarda Püntener

The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but the ...

AMER CHEMICAL SOC2023

Metabolic dependencies of metastasis-initiating cells in female breast cancer

Albert Santamaria Martinez, Pierre Vincent Dessen, Jörg Hülsken, Laurent Nam Ky Beziaud, Angela Madurga Alonso, Candice Megan T Young

Understanding the mechanisms that enable cancer cells to metastasize is essential in preventing cancer progression. Here we examine the metabolic adaptations of metastasis-initiating cells (MICs) in female breast cancer and how those shape their metastatic ...

Nature Portfolio2023

Mechanism of KRAS-driven T cell infiltration in colorectal cancer

Amber Dawn Bowler

Colorectal cancer is the second-leading cause of cancer death worldwide. Early-stage disease can be detected with preventative medical screening and is treatable with surgical resection. Sixty-percent of patients, however, are diagnosed with advanced-stage ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

Andrea Cavalli

Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or pr ...

FRONTIERS MEDIA SA2023

Medical and Personal Characteristics Can Predict the Risk of Lung Metastasis

Michele De Palma, Nahal Mansouri

Aims: Understanding the correlations between underlying medical and personal characteristics of a patient with cancer and the risk of lung metastasis may improve clinical management and outcomes. We used machine learning methodologies to predict the risk o ...

2023

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

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

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Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

Andrea Cavalli

FRONTIERS MEDIA SA2023

Medical and Personal Characteristics Can Predict the Risk of Lung Metastasis

Michele De Palma, Nahal Mansouri

2023

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

Hamed Khakzad

PUBLIC LIBRARY SCIENCE2023

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

Irina Märki

EPFL2023