Maxime Ulysse Garcia

Maxime Ulysse Garcia
Karolinska Institutet | KI · Department of Oncology-Pathology

PhD

About

16
Publications
3,502
Reads
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417
Citations
Introduction
After a PhD in Marseille, and a post-doc in Singapour, I'm now in Stockholm, working for the Childhood Tumor Biobank (Barntumörbanken) at Karolinska Institutet. I'm developing Sarek, a WGS/WES analysis pipeline in Nextflow, in collaboration with infrastructures within Science for Life Laboratory. I’m interested in Reproducible Research, Automation, Data Integration, Visualization and much more...
Additional affiliations
April 2016 - present
Karolinska Institutet
Position
  • Bioinformatician
April 2013 - April 2014
National University of Singapore
Position
  • Research Associate
September 2009 - February 2013
Institut Paoli Calmettes
Position
  • PhD Student
Education
September 2009 - December 2013
Aix-Marseille Université
Field of study
  • Bioinformatics and Genomics
September 2007 - June 2009
Aix-Marseille Université
Field of study
  • Bioinformatics, Structural Biochemistry and Genomics
September 2004 - June 2007
Aix-Marseille Université
Field of study
  • Life Science / Biochemistry

Publications

Publications (16)
Article
Full-text available
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeli...
Article
Full-text available
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and s...
Preprint
Full-text available
The broadening utilisation of ancient DNA (aDNA) to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned pipeline for the an...
Article
Full-text available
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and s...
Preprint
Full-text available
The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Bioinformatic analysis pipelines are often designed for execution on-premise, and this inevitably leads to a level of customisation and integration that is only applicable to the local infrastructure. More notably,...
Conference Paper
Full-text available
Introduction Whole-genome sequencing of cancer tumours is more a research tool nowadays, but going to be used in clinical settings in the near future to facilitate precision medicine. While large institutions have built up in-house bioinformatics solutions for their own data analysis, robust and portable workflows combining multiple software have b...
Preprint
Full-text available
Whole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide va...
Article
Full-text available
The Na+/Ca2+exchanger (NCX) is a membrane antiporter that has been identified in the plasma membrane, the inner membrane of the nuclear envelope and in the membrane of the endoplasmic reticulum (ER). In humans, three genes have been identified, encoding unique NCX proteins. Although extensively studied, the NCX's sub-cellular localization and mecha...
Article
With the development of high-throughput gene expression profiling technologies came the opportunity to define genomic signatures predicting clinical condition or cancer patient outcome. However, such signatures show dependency on training set, lack of generalization, and instability, partly due to microarray data topology. Additional issues for ana...
Article
Full-text available
Pancreatic Ductal Adenocarcinoma (PDAC) is a very aggressive malignancy characterized by an excessive resistance to all known anticancer therapies, a still largely elusive phenomenon. In order to identify original mechanisms, we have explored the role of post-translational modifications (PTMs) mediated by members of the ubiquitin family. Though alt...
Chapter
Full-text available
The introduction of high-throughput gene expression profiling technologies (DNA microarrays) in molecular biology and their expected applications to the clinic have allowed the design of predictive signatures linked to a particular clinical condition or patient outcome in a given clinical setting. However, it has been shown that such signatures are...
Conference Paper
Full-text available
Background / Purpose: High-throughput gene expression profiling technologies yield genomic signatures to predict clinical condition or patient outcome. However, such signatures have limitations, such as dependency on training set and lack of generalization.We propose a novel algorithm, ITI (Interactome-Transcriptome Integration) (1), to extract a...
Article
Full-text available
High-throughput gene expression profiling yields genomic signatures that allow the prediction of clinical conditions including patient outcome. However, these signatures have limitations, such as dependency on the training set, and worse, lack of generalization. We propose a novel algorithm called ITI (interactome-transcriptome integration), to ext...

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Projects

Projects (3)
Project
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Project
An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing