Marco Trevisan-Herraz

Marco Trevisan-Herraz
Newcastle University | NCL · Institute of Cellular Medicine

PhD

About

32
Publications
2,535
Reads
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498
Citations
Citations since 2017
20 Research Items
368 Citations
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2017201820192020202120222023020406080
2017201820192020202120222023020406080
2017201820192020202120222023020406080
Additional affiliations
October 2011 - present
Spanish National Centre for Cardiovascular Research
Position
  • Bioinformatician
December 2008 - September 2011
Centro De Biología Molecular Severo Ochoa
Position
  • pre doctoral researcher

Publications

Publications (32)
Article
Chromosomal translocations are important drivers of hematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus ( IGH ) and proto-oncogene CCND1 that are...
Article
Full-text available
Changes in melanocytic naevi and development of new naevi have been reported in pregnant women. The association between pregnancy and melanoma is a controversial topic. We conducted this review to identify the dermatoscopic changes that occur in naevi during pregnancy that could facilitate in distinguishing benign from suspicious lesions. Medline,...
Preprint
Full-text available
Topologically associated domains (TADs) are interaction sub-networks of 3D genomes. TAD boundaries frequently coincide with genome breaks while their deletion is under negative selection, suggesting that TADs act as modules facilitating genome rearrangements and metazoan evolution. However, the role of TADs in the evolution of gene regulation and e...
Preprint
Full-text available
Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called super-enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the enhancers of the immunoglobulin heavy chain locus (IGH) and proto-oncogene CCND1 tha...
Article
Full-text available
Changes in the oxidation state of protein Cys residues are involved in cell signalling and play a key role in a variety of pathophysiological states. We had previously developed GELSILOX, an in-gel method that enables the large-scale, parallel analysis of dynamic alterations to the redox state of Cys sites and protein abundance changes. Here we pre...
Article
Full-text available
Macrophages are involved in the primary human response to Candida albicans. After pathogen recognition signaling pathways are activated, leading to the production of cytokines, chemokines and antimicrobial peptides. ATP binding proteins are crucial for this regulation. Here, a quantitative proteomic and phosphoproteomic approach was carried out for...
Article
Full-text available
Adult cardiac progenitor/stem cells (CPC/CSC) are multipotent resident populations involved in cardiac homeostasis and heart repair. Assisted by complementary RNAseq analysis, we defined the fraction of the CPC proteome associable with specific functions by comparison with human bone marrow mesenchymal stem cells (MSC), the reference population for...
Article
Full-text available
Mass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software package for the statistical analysis of high-throughput, quantitative proteomics experiments. SanXoT is based o...
Article
Full-text available
Post-translational modifications hugely increase the functional diversity of proteomes. Recent algorithms based on ultratolerant database searching are forging a path to unbiased analysis of peptide modifications by shotgun mass spectrometry. However, these approaches identify only one-half of the modified forms potentially detectable and do not ma...
Preprint
Full-text available
Post-translational modifications hugely increase the functional diversity of proteomes. Recent algorithms based on ultratolerant database searching are forging a path to unbiased analysis of peptide modifications by shotgun mass spectrometry. However, these approaches identify only half of the modified forms potentially detectable and do not map th...
Preprint
Full-text available
In most software tools for quantification of mass spectrometry-based proteomics by stable isotope labelling (SIL), there is a recurrent disconnection between the use of a statistical model and convenient data visualisation to check correct data modelling. Most of them lack a robust statistical framework, using models which do not account for the ma...
Chapter
Mass spectrometry-based proteomics using soft ionization techniques has been used successfully to identify large numbers of proteins from complex biological samples. However, reproducible quantification across a large number of samples is still highly challenging with commonly used "shotgun proteomics" which uses stochastic sampling of the peptide...
Article
Full-text available
High-density lipoproteins (HDLs) are complex protein and lipid assemblies whose composition is known to change in diverse pathological situations. Analysis of the HDL proteome can thus provide insight into the main mechanisms underlying abdominal aortic aneurysm (AAA) and potentially detect novel systemic biomarkers. We performed a multiplexed quan...
Working Paper
Full-text available
Guillain-Barré syndrome (GBS) is an autoimmune-mediated peripheral neuropathy of unknown cause. However, about a quarter of GBS patients have suffered a recent bacterial or viral infection, and axonal forms of the disease are especially common in these patients. Proteomics is a good methodological approach for the discovery of disease biomarkers. U...
Article
Full-text available
The coordinated behavior of proteins is central in systems biology; however the underlying mechanisms are poorly known and methods to analyze coordination by conventional quantitative proteomics are still lacking. We present the Systems Biology Triangle (SBT), a new algorithm that allows the study of protein coordination by pairwise quantitative pr...
Article
Peptide identification is increasingly achieved through database searches in which mass precursor tolerance is set in the ppm range. This trend is driven by the high resolution and accuracy of modern mass spectrometers and the belief that the quality of peptide identification is fully controlled by estimating the false discovery rate (FDR) using th...
Article
Recent findings support potential roles for HDL in cardiovascular pathophysiology not related to lipid metabolism. We address whether HDL proteome is dynamically altered in atheroma plaque rupture. We used immunoaffinity purification of HDL samples from coronary artery disease patients before and after percutaneous transluminal coronary angioplasty...
Article
The combination of stable isotope labeling (SIL) with mass spectrometry (MS) allows comparison of the abundance of thousands of proteins in complex mixtures. However, interpretation of the large data sets generated by these techniques remains a challenge because appropriate statistical standards are lacking. Here, we present a generally applicable...
Article
Proteins secreted by cells are of the highest biomedical relevance since they play a significant role in the progression of numerous diseases. However, characterization of the proteins specifically secreted in response to precise stimuli is challenging, since these proteins are contaminated by cellular byproducts. Here we present a method to charac...
Article
Full-text available
MS-based quantitative proteomics plays an increasingly important role in biological and medical research and the development of these techniques remains one of the most important challenges in mass spectrometry. Numerous stable isotope labeling approaches have been proposed. However, and particularly in the case of (18)O-labeling, a standard protoc...
Conference Paper
Background / Purpose: Analysis of conventional proteomics results involves multiple steps; including experiment creation into the OmicsHub database, data importation, data filtering, protein/peptide identification, validation, quantification, statistical analysis and creation of the final report. This workflow usually requires usage of many diffe...

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