@article {2019|2079,
	title = {Molecular Graphics: Bridging Structural Biologists and Computer Scientists.},
	journal = {Structure},
	volume = {27},
	year = {2019},
	month = {2019 11 05},
	pages = {1617-1623},
	abstract = {<p>Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.</p>
},
	issn = {1878-4186},
	doi = {10.1016/j.str.2019.09.001},
	author = {Martinez, Xavier and Krone, Michael and Alharbi, Naif and Rose, Alexander S and Laramee, Robert S and O{\textquoteright}Donoghue, Sean and Marc Baaden and Chavent, Matthieu}
}
@article {2018|2091,
	title = {MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.},
	journal = {J Integr Bioinform},
	volume = {15},
	year = {2018},
	month = {2018 Jun 21},
	abstract = {<p>Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.</p>
},
	keywords = {Algal Proteins, Chlamydomonas reinhardtii, Computer Graphics, Imaging, Three-Dimensional, Models, Structural, Oxidation-Reduction, Protein Conformation, Protein Interaction Maps, Protein Processing, Post-Translational, Proteome, Proteomics, Software, Virtual Reality},
	issn = {1613-4516},
	doi = {10.1515/jib-2018-0006},
	author = {Maes, Alexandre and Martinez, Xavier and Druart, Karen and Laurent, Benoist and Gu{\'e}gan, Sean and Marchand, Christophe H and Lemaire, St{\'e}phane D and Marc Baaden}
}
@conference {2017|2101,
	title = {Molecular Visualization of Computational Biology Data: A Survey of Surveys},
	booktitle = {EuroVis 2017 - Short Papers},
	year = {2017},
	publisher = {The Eurographics Association},
	organization = {The Eurographics Association},
	isbn = {978-3-03868-043-7},
	doi = {10.2312/eurovisshort.20171146},
	author = {Alharbi, Naif and Alharbi, Mohammad and Martinez, Xavier and Krone, Michael and Rose, Alexander S. and Marc Baaden and Laramee, Robert S. and Chavent, Matthieu},
	editor = {Barbora Kozlikova and Tobias Schreck and Thomas Wischgoll}
}
