M
Maxime Garcia
Researcher at Karolinska Institutet
Publications - 30
Citations - 997
Maxime Garcia is an academic researcher from Karolinska Institutet. The author has contributed to research in topics: Pipeline (software) & Interactome. The author has an hindex of 6, co-authored 30 publications receiving 354 citations. Previous affiliations of Maxime Garcia include French Institute of Health and Medical Research & University of Lyon.
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Journal ArticleDOI
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels,Alexander Peltzer,Sven Fillinger,Harshil Patel,Johannes Alneberg,Andreas Wilm,Maxime Garcia,Paolo Di Tommaso,Sven Nahnsen +8 more
TL;DR: The nf-core framework is introduced as a means for the development of collaborative, peerreviewed, best-practice analysis pipelines that can be used across all institutions and research facilities and introduces a higher degree of portability as compared to custom in-house scripts.
Journal ArticleDOI
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
Maxime Garcia,Szilveszter Juhos,Szilveszter Juhos,Malin Larsson,Pall I Olason,Marcel Martin,Jesper Eisfeldt,Sebastian DiLorenzo,Johanna Sandgren,Teresita Díaz de Ståhl,Philip Ewels,Valtteri Wirta,Monica Nistér,Max Käller,Björn Nystedt +14 more
TL;DR: Sarek is an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels that offers easy, efficient, and reproducible WGS analyses.
Posted ContentDOI
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Maxime Garcia,Szilveszter Juhos,Malin Larsson,Pall I Olason,Marcel Martin,Jesper Eisfeldt,Sebastian DiLorenzo,Johanna Sandgren,Teresita Díaz de Ståhl,Valtteri Wirta,Monica Nistér,Björn Nystedt,Max Käller +12 more
TL;DR: Sarek is a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples.
Posted ContentDOI
nf-core: Community curated bioinformatics pipelines
Philip Ewels,Alexander Peltzer,Sven Fillinger,Alneberg J,Harshil Patel,Andreas Wilm,Maxime Garcia,Di Tommaso P,Sven Nahnsen +8 more
TL;DR: The nf-core framework as discussed by the authors provides a community-driven platform for the creation and development of best practice analysis pipelines written in the Nextflow language, which can be used across various institutions and research facilities.
Journal ArticleDOI
Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins.
Thomas Bonacci,Stéphane Audebert,Luc Camoin,Emilie Baudelet,Ghislain Bidaut,Maxime Garcia,Ini Isabée Witzel,Neil D. Perkins,Jean-Paul Borg,Juan L. Iovanna,Philippe Soubeyran +10 more
TL;DR: The role of post-translational modifications (PTMs) mediated by members of the ubiquitin family are explored and gemcitabine-induced PTMs variations of relevant candidates are validated and the biological significance of such altered PTMs is demonstrated by studying in detail the sumoylation of SNIP1, one of these new targets.