Christophe Magnan - University of California, Irvine

Profile

Research Areas
Technical Skills
Collaborative Work
Academic Summary
Education Summary
Contact Information
Google Scholar Profile

Research Areas

Bioinformatics - my primary center of interest is the design and development of novel computational methods capable of either predicting, extracting, or identifying relevant biological results from relatively large amounts of data generated for that purpose.

Genomics - high-throughput sequencing data analysis for various applications of the technology (genome assembly, small/large variations, gene expression, alternative splicing, circadian rhythm, base modification, cancer research, personalized medicine) & sequencing platforms (Illumina, PacBio, Complete Genomics).

Proteomics - sequence-based prediction of protein's structural features or global properties using machine learning and homology/template-based methods. I am notably interested in studying how the two approaches can be combined together to increase the overall accuracy of the resulting predictors.

Machine Learning - I have an on-and-off interest in studying methods for non-classic learning contexts like semi-supervised learning, learning from data corrupted by classification noise, multi-class learning, and learning from sequential or spatial data, primarily motivated by their potential use in proteomics.

Technical Skills

Programming - I am an advanced programmer in Perl, C, C++, and Java with numerous programs already written in these languages. I have a solid knowledge of Bash, MySQL, PHP, JS, and HTML due to a regular need for these languages in my work. I occasionally work with R, CGI, Ajax, jQuery, Python, Pascal, and Latex.

Environment - I have been working for 15 years on Unix-based operating systems (Linux distributions and Mac OS) and for 11 years on a relatively large computational grid (1000+ cores) with a distant file server. I work routinely with the SGE job scheduler and have experience in parallel/distributed computing.

Collaborative Work

The Institute for Genomics and Bioinformatics (Pierre Baldi, Director and P.I.) collaborates with many research groups in the areas of Biology, Medicine, Chemistry, Physics, Computer Science, or Mathematics, and contributes regularly to the projects of these groups with its expertise in machine learning and bioinformatics.

I am actively involved in several of these collaborations and the corresponding projects represent a large part of my research work in genomics so I listed below some of the most significant collaborations I participated in together with a brief description of the research activities of each group. The list includes past collaborations.

Marcelo Wood's Lab, Department of Neurobiology and Behavior, School of Biological Sciences, UCI.
Molecular mechanisms underlying long-term memory processes, age-related memory impairments.

Suzanne Sandmeyer's Lab, Department of Biological Chemistry, School of Medicine, UCI.
Molecular genetics and biochemistry of retrotransposons and metabolic engineering in yeast.

Leonard Sender, Chao Family Comprehensive Cancer Center, Hyundai Cancer Inst., CHOC Children’s.
Pediatric cancer research, oncology treatment, genomic cancer research, cancer survivorship.

Trina Norden-Krichmar's Lab, Department of Epidemiology, School of Medicine, UCI.
Genetic factors in human diseases, computational drug discovery, alcoholic liver diseases.

Paolo Sassone-Corsi's Lab, Center for Epigenetics and Metabolism, School of Medicine, UCI.
Mechanisms of signal transduction, gene expression, epigenetics, circadian clock.

Marquis Philip Vawter's Lab, Department of Psychiatry & Human Behavior, School of Medicine, UCI.
Genetic and molecular basis of neuropsychiatric disorders (schizophrenia and mood disorders).

Timothy Bredy's Lab, Queensland Brain Institute, University of Queensland.
Epigenetic mechanisms contribution to the long-term memories, psychiatric disorders.

Tommaso Pizzorusso's Lab, Department of Neuroscience, University of Florence.
Development of the visual cortex, regulation of critical periods of brain development.

Academic Summary

●	Since July	Institute for Genomics and Bioinformatics University of California, Irvine	Associate Project Scientist	Research in bioinformatics (genomics & proteomics)
●	Since 2010	Genomics High-Throughput Facility University of California, Irvine	Sequencing Systems Data Administrator	Overseeing storage, processing, and analysis of the sequencing data generated by the facility
●	2013- 2019	Institute for Genomics and Bioinformatics University of California, Irvine	Assistant Project Scientist	Research in bioinformatics (genomics & proteomics)
●	2008- 2013	Institute for Genomics and Bioinformatics University of California, Irvine	Postdoctoral Fellow	Research in bioinformatics (genomics & proteomics)
●	2007- 2008	Laboratoire d'Informatique Fondamentale Université de Provence	Research & Teaching Assistant	Research in machine learning and bioinformatics, teaching
●	2004- 2007	Laboratoire d'Informatique Fondamentale Université de Provence	PhD Student & Teaching Assistant	Research in machine learning and bioinformatics, teaching

Education Summary

●	2004-2007	Université de Provence Château-Gombert, Marseille	Doctorat Informatique	Doctor's Degree
●	2003-2004	Université de Provence Luminy, Marseille	DEA Informatique	Master's Degree
●	2002-2003	Université de Provence Château-Gombert, Marseille	Maitrise Informatique	Master's Degree
●	2001-2002	Université de Provence Château-Gombert, Marseille	Licence Informatique	Bachelor's Degree
●	1999-2001	Université de Provence Saint-Charles, Marseille	DEUG MIAS	Bachelor's Degree

Contact Information

Christophe Magnan
Institute for Genomics and Bioinformatics
249 Information and Computer Science 2
University of California, Irvine
Irvine, CA 92697-3445, USA

cmagnan@ics.uci.edu