Christophe Magnan

Institute for Genomics and Bioinformatics
School of Information & Computer Sciences
University of California, Irvine

Publications

• Refereed Journals
• Refereed Conference Proceedings
• French National Journals & Conferences
• Short Papers, Posters, Other Manuscripts
• Google Scholar Profile

Refereed Journals

• Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. K. Patterson, F. Shavarebi, C.N. Magnan, I. Chang, X. Qi, P. Baldi, V. Bilanchone, S.B. Sandmeyer. Genome Research, 29(8), 1298-1309, 2019.


• Defining the Independence of the Liver Circadian Clock. K.B. Koronowski, K. Kinouchi, P.S. Welz, J.G. Smith, V.M. Zinna, J. Shi, M. Samad, S. Chen, C.N. Magnan, J.M. Kinchen, W. Li, P. Baldi, S. Benitah, P. Sassone-Corsi. Cell, 177(6), 1448-1462, 2019.


• The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction. X. Li, Q. Zhao, W. Wei, Q. Lin, C.N. Magnan, M.R. Emami, L.E. Wearick-Silva, T.W. Viola, P.R. Marshall, J. Yin, S.U. Madugalle, Z. Wang, S. Nainar, C.B. Vågbø, L.J. Leighton, E.L. Zajaczkowski, K. Ke, R. Grassi-Oliveira, M. Bjørås, P.F. Baldi, R.C. Spitale, T.W. Bredy. Nature Neuroscience, 22(4), 534-544, 2019.


• Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. K. Kinouchi, C.N. Magnan, N. Ceglia, Y. Liu, M. Cervantes, N. Pastore, T. Huynh, A. Ballabio, P. Baldi, S. Masri, P. Sassone-Corsi. Cell Reports, 25(12), 3299-3314.e6, 2018.


• Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory. J.L. Kwapis, Y. Alaghband, E.A. Kramár, A.J. López, A. Vogel-Ciernia, A.O. White, G. Shu, D. Rhee, C.M. Michael, E. Montellier, Y. Liu, C.N. Magnan, S. Chen, P. Sassone-Corsi, P. Baldi, D.P. Matheos, M.A. Wood. Nature Communications, 9, 3323, 2018.


• Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception. R. Mazziotti, L. Baroncelli, N. Ceglia, G. Chelini, G. Della Sala, C.N. Magnan, D. Napoli, E. Putignano, D. Silingardi, J. Tola, P. Tognini, J.S.C. Arthur, P. Baldi, T. Pizzorusso. Nature Communications, 8, 15488, 2017.


• Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling. A. Vogel-Ciernia, E.A. Kramár, D.P. Matheos, R. Havekes, T.J. Hemstedt, C.N. Magnan, K. Sakata, A. Tran, S. Azzawi, A. Lopez, R. Dang, W. Wang, B. Trieu, J. Tong, R.M. Barrett, R.J. Post, P. Baldi, T. Abel, G. Lynch, M.A. Wood. Learning & Memory, 24(5), 199-209, 2017.


• ClusterCAD: a computational platform for type I modular polyketide synthase design. C.H. Eng, T.W.H. Backman, C.B. Bailey, C.N. Magnan, H.G. Martín, L. Katz, P. Baldi, J.D. Keasling. Nucleic Acids Research, 46(D1), D509-D515, 2017.


• Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity. C.N. Magnan, J. Yu, I. Chang, E. Jahn, Y. Kanomata, J. Wu, M. Zeller, M. Oakes, P. Baldi, S. Sandmeyer. PLOS ONE, 11(9), e0162363, 2016.


• VIRALpro: a tool to identify viral capsid and tail sequences. C. Galiez, C.N. Magnan, F. Coste, P. Baldi. Bioinformatics, 32(9), 1405-1407, 2016.


• Mitochondrial Mutations in Subjects with Psychiatric Disorders. A. Sequeira, B. Rollins, C.N. Magnan, M. van Oven, P. Baldi, R.M. Myers, J.D. Barchas, A.F. Schatzberg, S.J. Watson, H. Akil, W.E. Bunney, M.P. Vawter. PLOS ONE, 10(5), e0127280, 2015.


• A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. M. Zeller, C.N. Magnan, V.R. Patel, P. Rigor, L. Sender, P. Baldi. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(5), 826-839, 2014.


• SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. C.N. Magnan, P. Baldi. Bioinformatics, 30(18), 2592-2597, 2014.


• The Neuron-Specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory. A. Vogel-Ciernia, D.P. Matheos, R.M. Barrett, E. Kramár, S. Azzawi, Y. Chen, C.N. Magnan, M. Zeller, A. Sylvain, J. Haettig, Y. Jia, A. Tran, R. Dang, R.J. Post, M. Chabrier, A. Babayan, J.I. Wu, G.R. Crabtree, P. Baldi, T.Z. Baram, G. Lynch, M.A. Wood. Nature Neuroscience, 16(5), 552-561, 2013.


• Mitochondrial Mutations and Polymorphisms in Psychiatric Disorders. A. Sequeira, M.V. Martin, B. Rollins, E.A. Moon, W.E. Bunney, F. Macciardi, S. Lupoli, E.N. Smith, J. Kelsoe, C.N. Magnan, M. van Oven, P. Baldi, D.C. Wallace, M.P. Vawter. Frontiers in Genetics, 3, 103, 2012.


• High-throughput prediction of protein antigenicity using protein microarray data. C.N. Magnan, M. Zeller, M.A. Kayala, A. Vigil, A. Randall, P.L. Felgner, P. Baldi. Bioinformatics, 26(23), 2936-2943, 2010.


• SOLpro: accurate sequence-based prediction of protein solubility. C.N. Magnan, A. Randall, P. Baldi. Bioinformatics, 25(17), 2200-2207, 2009.

Refereed Conference Proceedings

• A Protocol to Detect Local Affinities Involved in Proteins Distant Interactions. C.N. Magnan, C. Capponi, F. Denis. Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), San Jose, CA, USA, November 2007. IEEE Press, isbn 0-7695-3031-1, 252-257, 2007.


• Efficient Learning of Naive Bayes Classifiers under Class-Conditional Classification Noise. F. Denis, C.N. Magnan, L. Ralaivola. Proceedings of the 23rd International Conference on Machine Learning (ICML 2006), Pittsburgh, PA, USA, June 2006. ACM Press, isbn 1-59593-383-2, 265-272, 2006.


• CN = CPCN. L. Ralaivola, F. Denis, C.N. Magnan. Proceedings of the 23rd International Conference on Machine Learning (ICML 2006), Pittsburgh, PA, USA, June 2006. ACM Press, isbn 1-59593-383-2, 721-728, 2006.

French National Journals & Conferences

• Asymmetrical Semi-Supervised Learning and Prediction of Disulfide Connectivity in Proteins. C.N. Magnan. Revue d'Intelligence Artificielle, 20(6), 673-695, 2006.


• Apprentissage de classifieurs naïfs de Bayes à partir de données soumises à un bruit de classification conditionnel à chaque classe. F. Denis, C.N. Magnan, L. Ralaivola. Actes de la 8ème Conférence Francophone sur l'Apprentissage Automatique (CAp 2006), Trégastel, France, May 2006. PUG Press, isbn 2-7061-1372-3, 251-266, 2006.


• Bruits de classification constant et constant par morceaux : égalité des ensembles de classes de concepts apprenables. L. Ralaivola, F. Denis, C.N. Magnan. Actes de la 8ème Conférence Francophone sur l'Apprentissage Automatique (CAp 2006), Trégastel, France, May 2006. PUG Press, isbn 2-7061-1372-3, 235-250, 2006.


• Apprentissage semi-supervisé asymétrique et estimations d'affinités locales dans les protéines. C.N. Magnan. Actes de la 7ème Conférence Francophone sur l'Apprentissage Automatique (CAp 2005), Nice, France, June 2005. PUG Press, isbn 2-7061-1319-7, 297-312, 2005.

Short Papers, Posters, Other Manuscripts

• [Poster] Gene Expression Profiling of PBMCs in Alcoholic and Non‐Alcoholic Liver Diseases. T.M. Norden‐Krichmar, S. Listopad, N. Siddiqui, C.N. Magnan, Z.X. Liu, J.M. Jacobs, T.R. Morgan, Southern California Alcoholic Hepatitis Consortium (SCAHC). HEPATOLOGY, 68, 781A, 2018.


• [Poster] Transcriptomics of liver tissue, PBMCs, and monocytes in alcoholic hepatitis. T.M. Norden-Krichmar, C.N. Magnan, Z.X. Liu, J.M. Jacobs, T.R. Morgan. HEPATOLOGY, 66, 705A, 2017.


• [Poster] Un protocole de détection d'affinités locales dans les protéines. C.N. Magnan, C. Capponi, F. Denis. Actes de la 9ème Conférence Francophone sur l'Apprentissage Automatique (CAp 2007), Grenoble, France, July 2007. Cépaduès Editions, isbn 978-2-85428-789-9, 299-300, 2007.


• [PhD Thesis] Apprentissage à partir de données diversement étiquetées pour l'étude du rôle de l'environnement local dans les interactions entre acides aminés. C.N. Magnan. Supervised by François Denis and Cécile Capponi. Université de Provence, Aix-Marseille I, December 2007.