Thesis • Articles • Correspondences • Preprints • Chapters • Talks • Posters • Scientific animation workshop
Thesis
  • • Garcia MU, Biomarkers discovery in breast cancer by Interactome-Transcriptome Integration, 2013/12/20.
Articles
  • • Fellows Yates​ JA, Lamnidis TC, Borry M, Valtueña AA, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer​ A, Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager, PeerJ 9:e10947.
  • • Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren S, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B, Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved], F1000Research (2020), 9:63.
  • • Liu T, Zhao J, Ibarra C, Garcia U. M, Uhlén P, Nistér M, Glycosylation Controls Sodium-Calcium Exchanger 3 Sub-Cellular Localization During Cell Cycle, European Journal of Cell Biology (2018) 97 (3): 190-203.
  • • Bonacci T, Audebert S, Camoin L, Baudelet E, Bidaut G, Garcia MU, Witzel II, Perkins ND, Borg JP, Iovanna JL, Soubeyran P, Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins, Journal of Proteome Research (2014) 13 (5): 2478–2494.
  • • Garcia MU, Millat-Carus R, Bertucci F, Finetti P, Birnbaum D, Bidaut G, Interactome-transcriptome integration for predicting distant metastasis in breast cancer, Bioinformatics (2012) 28 (5): 672-678.
Correspondences
  • • Ewels P, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S, The nf-core framework for community-curated bioinformatics pipelines, Nat Biotechnol (2020).
Preprints
  • • Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagneräs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A, Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager, bioRxiv 2020.06.11.145615.
  • • Ewels P, Peltzer A, Fillinger S, Alneberg J, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S, nf-core: Community curated bioinformatics pipelines, bioRxiv 610741.
  • • Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Diaz de Ståhl T, Wirta V, Nistér M, Nystedt B, Käller M, Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants, bioRxiv 316976.
Chapters
  • • Garcia MU, Millat-Carus R, Bertucci F, Finetti P, Guille A, Adelaïde J, Bekhouche I, Sabatier R, Chaffanet M, Birnbaum D, Bidaut G, CNV-Interactome-Transcriptome Integration to detect driver genes in cancerology in Microarray Image and Data Analysis: Theory and Practice, CRC Press (2014) 12: 331-338.
  • • Garcia MU, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Detection of driver protein complexes in breast cancer metastasis by large scale transcriptome-interactome integration, Methods in Molecular Biology (2014) 1101: 67-85.
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Linking Interactome to Disease: A Network-Based Analysis of Metastatic Relapse in Breast Cancer in Bioinformatics: Concepts, Methodologies, Tools, and Applications. IGI Global, (2013): 151-172.
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Linking Interactome to Disease: A Network-Based Analysis of Metastatic Relapse in Breast Cancer in Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, IGI Global (2011): 406-427.
Talks
  • • Garcia MU, CbioNet - What is nf-core?, online, 2022/04.
  • • Garcia MU, nf-core/bytesize #34 - Bytesize 34: Updates on the new DSL2 syntax Talk, online, 2022/02. nf-core/bytesize #34
  • • Garcia MU, nf-core/bytesize #18 - Development Environments and Workflows, online, 2021/06. nf-core/bytesize #18
  • • Garcia MU, nf-core/bytesize #8 - Running pipelines offline, online, 2021/04. nf-core/bytesize #8
  • • Garcia MU, nf-core/bytesize #2 - How nf-core configs work, online, 2021/02. nf-core/bytesize #2
  • • Garcia MU, nf-core Hackathon - Featured nf-core pipelines: Sarek, Heidelberg, Germany, 2020/07. nf-core Hackathon July 2020
  • • Garcia MU, nf-core a community effort for collaborative peer-reviewed pipelines, Montpellier, France, 2020/06-07. JOBIM 2020
  • • Garcia MU, CI⋆Joe - Make your code great again, Stockholm, Sweden, 2020/05. Coffee n' Code Club
  • • Garcia MU, Sarek, a workflow to detect germline and somatic mutations in WGS/WES, Bergen, Norway, 2019/10. 4th Scandinavian Seminar on Translational Pathology
  • • Garcia MU, Sarek, A portable workflow for WGS/WES analysis of germline and somatic mutations, Stockholm, Sweden, 2018/10. FoUU-day for clinical pathology-cytology
  • • Garcia MU, Sarek, a portable workflow for WGS analysis of germline and somatic mutations, Marseille, France, 2018/07. JOBIM 2018
  • • Garcia MU, Sarek and nf-core for Reproducibility, Basel, Switzerland, 2018/03. SPHN Workflow Interoperability Workshop
  • • Garcia MU, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, Vienna, Austria, 2011/04. MASAMB XXI
  • • Garcia MU, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, Cambridge, UK, 2010/09. Cancer Bioinformatics Whorkshop videolectures.net
Posters
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Ewels P, Nystedt B, Nistér M, Käller M, Sarek, a workflow for WGS analysis of germline and somatic mutations, Stockholm, Sweden, 2018/08. Department Kick Off 2018
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Ewels P, Nystedt B, Nistér M, Käller M, Sarek, a workflow for WGS analysis of germline and somatic mutations, Reykjavìk, Iceland, 2018/06. The Nordic Precision Medicine Initiative
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Ewels P, Nystedt B, Nistér M, Käller M, Sarek, a workflow for WGS analysis of germline and somatic mutations, Stockholm, Sweden, 2018/05. Keystone Symposia - Precision Medicine in Cancer (E1)
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Ewels P, Nystedt B, Nistér M, Käller M, Sarek, a workflow for WGS analysis of germline and somatic mutations, Stockholm, Sweden, 2018/03. Frontiers in Cancer Research and Therapy 2018
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Nystedt B, Nistér M, Käller M, Cancer Analysis Workflow to process normal/tumor WGS data, Stockholm, Sweden, 2017/08. Department Kick Off 2017
  • • Garcia MU, Juhos S, Larsson M, Diaz de Ståhl T, Sandgren S, Eisfeldt J, DiLorenzo S, M Martin, Olason P, Nystedt B, Nistér M, Käller M, Cancer Analysis Workflow to process normal/tumor WGS data, Copenhagen, Denmark, 2017/05. European Human Genetics Conference 2017
  • • Garcia MU, Sahlén P, Diaz de Ståhl T, Eisfeldt J, Juhos S, DiLorenzo S, Larsson M, Olason P, Nystedt B, Nistér M, Käller M, Cancer Analysis Workflow Of Tumor/Normal Pairs At The National Genomics Infrastructure, Stockholm, Sweden, 2017/02. Frontiers in Cancer Research and Therapy 2017
  • • Garcia MU, Sahlén P, Diaz de Ståhl T, Eisfeldt J, Juhos S, DiLorenzo S, Larsson M, Olason P, Nystedt B, Nistér M, Käller M, Cancer Analysis Workflow Of Tumor/Normal Pairs At The National Genomics Infrastructure, Djurö, Sweden, 2016/09. The XVth KICancer Retreat 2016
  • • Garcia MU, Parent MA, Benoukraf T, Visualizing the DNA/DNA interactome using ChromoLens, Singapore, Singapore, 2013/11. Frontiers in Cancer Science 2013
  • • Garcia MU, Millat-Carus R, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Interactome-Transcriptome Integration Uncovers More Stable and Better Performing Biomarkers in Breast Cancer, Basel, Switzerland, 2012/09. ECCB 2012 - F1000
  • • Garcia MU, Millat-Carus R, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Interactome-Transcriptome Integration Uncovers More Stable and Better Performing Biomarkers in Breast Cancer, Rennes, France, 2012/07. JOBIM 2012
  • • Garcia MU, Millat-Carus R, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Interactome-Transcriptome Integration Uncovers More Stable and Better Performing Biomarkers in Breast Cancer, Marseille, France, 2012/02. 6ème Colloque du Cancéropôle PACA
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, Paris, France, 2011/07. JOBIM 2011
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, Marseille, France, 2011/06. 19th meeting of doctoral school
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, Marseille, France, 2010/12. BCP VII
  • • Garcia MU, Stahl O, Finetti P, Birnbaum D, Bertucci F, Bidaut G, Biomarkers Discovery in Breast Cancer by Interactome-Transcriptome Integration, St Raphaël, France, 2010/04. Interactomics: at the crossroads of biology and bioinformatics
Scientific animation workshop
  • • Colette Y, Betzi S, Garcia MU, La Chimie - base du Vivant, au service de la Recherche en Cancérologie, Marseille, France, 2011/10. Fête de la Science - Marché de la chimie