 Andrea Califano, Dr. Professor |
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Director, Center for the Multiscale Analysis of Genetic Networks (MAGNet)
Associate Director for Bioinformatics, Irving Cancer Research Center (ICRC)
Co-Director, Center for Computational Biology and Bioinformatics (C2B2)
Background
Dr. Califano's doctoral thesis in physics, at the University of Florence, was
on the behavior of high-dimensional dynamical systems . From 1986 to 1990, as a Research Staff Member in the Exploratory Computer Vision Group at the IBM TJ Watson Research Center he worked on several algorithms for machine learning, more specifically for the interpretation of 2D and 3D visual scenes.
In 1990 Dr. Califano started his activities in Computational Biology and, in 1997, became the program director of the IBM Computational Biology Center, a worldwide organization active in several research areas related to bioinformatics, chemoinformatics, complex biological system modeling/simulation, microarray analysis, protein structure prediction, and molecular-dynamics.
In 2000 he co-founded First Genetic Trust, Inc. to actively pursue translational genomics research and infrastructure related activities in the context of large-scale patient studies with a genetic components.
Finally, in 2003, he joined Columbia University.
His scientific interests lay in the investigation of Systems Biology, using a variety of physics and knowledge-based methods. Since 1998 he has been especially active in the development of integrative methodologies for the investigation of human B cell lymphomas. Specifically, he is interested in the reverse engineering of B cell cellular networks and in their use for the dissection of biological processes related to oncogenesis and tumor progression.
Research Interests
Andrea Califano
The Califano lab is interested in a variety of themes at the interface between the computational and the experimental biological sciences, including:
- The reverse engineering of gene regulatory and signaling networks in mammalian cellular contexts using information theoretic and machine learning methods followed by biochemical validation.
- The study of genetic modules that are disregulated in B a variety of human B cell malignanices using a systems biology approach.
- The application of systems biology methods to the dissection of complex normal and pathologic cellular phenotypes.
- The identification of cis-regulatory elements and modules in the non-coding genome of higher eukaryotes.
Selected Publications
- Stolovitzky GA, Monroe D, Califano A (2007) “ Dialogue on Reverse Engineering Assessment and Methods: the DREAM of high throughput pathway inference." Ann N Y Acad Sci. 2007 Oct 9;
- Margolin AA, Califano A (2007), “ Theory and limitations of genetic network inference from microarray data." Ann N Y Acad Sci. 2007 Oct 9;
- Mani K, Lefebvre C, Wang K, Lim WK, Margolin AA, Basso K, Dalla-Favera R, and Califano A (2007), “A Systems Biology Approach to the Identification of Causal Somatic Mechanisms in Cancer Phenotypes.” In Press, Proceedings of RECOMB Satellite Conference on Computational Cancer Biology, San Diego.
- Lefebvre C, Lim WK, Basso K, Dalla Favera R, and Califano A (2006), "A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells." Lecture Notes in Computer Science, Vol. 4532 Springer Verlag, ISBN: 978-3-540-73059-0. Also, Proceedings of the 2006 RECOMB Satellite Workshop on Systems Biology, San Diego.
- Lim WK, Wang K, Lefebvre C, Califano A “ Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks." Bioinformatics. 2007; 23(13): i282-8.
- Li Z, Zheng T, Califano A, and Floratos A (2007), “Pattern-based mining strategy to detect multi-locus association and gene environment interaction.” BMC Proceedings, 2007 1 (Suppl 1):S16.
- Sosinsky A., Honig B*, Mann R.S.* and Califano A (2007), “ Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting." Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10. Epub 2007 Mar 29
- Piccaluga PP, Agostinelli C, Califano A, Rossi M, Basso K, Zupo S, Went P, Klein U, Zinzani PL, Baccarani M, Dalla Favera R, Pileri SA. (2007), “ Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets." J Clin Invest. 2007 Mar;117(3):823-34
- Banerjee N. and Califano A, (2006) Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment- Independent Conservation Maps, 4th RECOMB Comparative Genomics Satellite Workshop, Montreal (CA).
- Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, O’Neal J, Neuberg D, Margolin AA, Weng A, Aster JC, Sigaux F, Soulier J, Look AT, Young R, Califano A and Ferrando A, (2006) NOTCH1 directly regulates MYC expression and controls oncogenic cell growth, in press, Proc. Natl. Acad. Sci USA.
- Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R and Califano A, (2006) ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context, BMC Bioinformatics;7(Suppl.1):S7, also arXiv.org/abs/q-bio.MN/0410037.
- Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A (2006). Reverse engineering cellular networks. Nature Protocols; 1(2): 662-671.
- Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A, (2006) Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes, in Proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB).
- Basso K, Margolin A, Stolovitzky G, Klein U, Dalla-Favera R, and Califano A, (2005) Reverse engineering of regulatory networks in human B cells, Nat Genet.;37(4):382-90.
- Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad Jr. H, Miljkovic V, Cattoretti G, Califano A, and Dalla-Favera R,"Transcriptional Analysis of the B Cell Germinal Center Reaction," Proceedings of the National Academy of Science, 2003.
- Liu A, Zhang X., Stolovitzky G, Califano A, and Firestein S, “Motif-Based Construction of a Functional Map for Mammalian Olfactory Receptors,” accepted paper, to appear in Genomics, 2003.
- Liu A and Califano A, “CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationship,” accepted paper, to appear in the Feb. 2003 issue of the Journal of Computational Biology.
- Klein U, Tu Y, Stolovitzky GA, Mattioli M, Cattoretti G, Husson H, Freedman A, Inghirami G, Cro L, Baldini L, Neri A, Califano A, Dalla-Favera R. “Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells.” J Exp Med. 2001 Dec 3;194(11):1625-38.. (* Both Dalla-Favera and Califano are senior authors)
- Califano A, Stolovitzky S and Tu Y, “Analysis of Gene Expression Microarrays for Phenotype Classification”, in Proceedings of the 8th Symposium on Intelligent Systems for Molecular Biology, San Diego, 2000.
- Hart R, Royyuru AK, Stolovitzky G, and Califano A, “Systematic and Automated Discovery of Protein Sequence Patterns,” in J Comput Biol. 2000;7(3-4):585-600. also in Proceedings of Fourth Annual International Conference on Computational Molecular Biology, Tokyo, 2000.
- Califano A, “Splash, Structural Pattern Localization Analysis by Sequential Histograms,” Bioinformatics. 2000 Apr;16(4):341-57.
- Califano A, Rigoutsos I: “FLASH: A Fast Look-up Algorithm for String Homology,” In Proc. of the 1st Int'l Conference on Intelligent Systems for Molecular Biology, pages 353--359, Bethesda, MD, July 1993.
- Califano A and Mohan R “Multidimensional indexing for recognizing visual shapes.” in. IEEE Transactions on Pattern Analysis and Machine Intelligence, 16(4):373--392, April 1994. Also in Proc. of 1991 IEEE Conf. on Comp. Vision and Pattern Recognition, Maui, June 1991