PUBLICATIONS and CONFERENCE PROCEEDINGS
Margolin AA*, Palomero T, Sumazin P, Califano A*, Ferrando A*, Stolovitzky G*
[ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes]
submitted (Nature Biotechnology)
Wang K, Saito M*, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R*, and Califano A*
[Genome-wide identification of transcriptional network modulators in human B cells]
submitted.
Carro MS*, Lim WK*, Snyder E, Colman H, Aldape K, Lasorella A, Califano A*, and Iavarone A*,
[A transcriptional regulatory network initiates and maintains the mesenchymal phenotype of human malignant glioma]
submitted
Mani K, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, and Califano A,
[A Systems Biology Approach to the Prediction of Causal Oncogenic Mechanisms and Drug Mechanism-of-Action Profiles in Cancer Phenotypes]
Molecular Systems Biology 4:169.
Piccaluga PP, Agostinelli C, Califano A, Carbone A, Fantoni L, Ferrari S, Gazzola A, Gloghini A, Righi S, Rossi M, Tagliafico E, Zinzani PL, Zupo S, Baccarani M, Pileri SA,
Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation
Cancer Res. 2007 Nov 15;67(22):10703-10.
Margolin A and Califano A,
Theory and Limitations of Genetic Network Inference from Microarray Data
Ann N Y Acad Sci. 2007 Oct 9.
Stolovitzky GA, Monroe D, Califano A,
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,
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,
A Systems Biology Approach to the Identification of Causal Mechanisms in Normal and Malignant Human B- Lymphocyte Phenotypes
Submitted to ISMB 2007
Lim WK, Wang K, Lefebvre C, and Califano A
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
Vol. 23 ISMB/ECCB 2007, pages i282-i288.
Margolin AA, Nemenman I, and Califano A
Multivariate dependence and genetic networks inference
Submitted to ISMB 2007
Lefebvre C, Lim WK, Basso K, Dalla Favera R, and Califano A
A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells
RECOMB Satellite Conference, San Diego, CA, 2006.
Image:Lefebvre et al Supplementary Table S1.xls
Image:Lefebvre et al Supplementary Table S2.xls
Piccaluga PP, Agostinelli C, Califano A, Rossi M, Basso K, Zupo S, Went P, Klein U, Zinzani PL, Baccarani M, Dalla Favera R, and Pileri SA
Gene Expression Analysis Of Peripheral T-Cell Lymphoma/Unspecified Reveals Distinct Profiles And New Potential Therapeutic Targets
Journal of Clinical Investigation, Volume 117, Number 3, Pages 823 - 834, 2007.
Banerjee N. and Califano A.
Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment- Independent Conservation Maps
4th RECOMB Comparative Genomics Satellite Worshop, Montreal (CA). 1996.
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
NOTCH1 directly regulates MYC expression and controls oncogenic cell growth
in press, Proc. Natl. Acad. Sci USA.
Poppema Sibrand, L Kluiver Joost, Atayar Cigdem, Berg Anke van den, Rosenwald Andreas, Hummel Michael, Lenze Dido, Lammert Hetty, Stein Harald, Joos Stephan, Barth Thomas, Dyer Martin, Lichter Peter, Klein Uwe, Cattoretti Giorgio, Gloghini Annunziata, Tu Yuhai, Stolovitzky Gustavo A, Califano Andrea, Carbone Antonino, Dalla-Favera Ricardo, Melzner Ingo, Bucur Alexandra J, Brüderlein Silke, Dorsch Karola, Hasel Cornelia, Barth Thomas FE, Leithäuser Frank, Möller Peter
Report: workshop on mediastinal grey zone lymphoma
European Journal Of Haematology
Volume 75 Page 45 - July 2005
doi:10.1111/j.1600-0609.2005.00454.x
Volume 75 Issue s66
Basso Katia, Margolin Adam A, Stolovitzky Gustavo, Klein Ulf, Dalla-Favera Riccardo, & Califano Andrea
Reverse engineering of regulatory networks in human B cells
Nature Genetics 37, 382 - 390 (2005)
Published online: 20 March 2005; | doi:10.1038/ng1532
Margolin Adam A., Nemenman Ilya, Basso Katia, Wiggins Chris, Stolovitzky Gustavo, Dalla-Favera Riccardo, Califano Andrea
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
Submitted to Bioinformatics, Sept. …, 2004 - arxiv.org
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A
Reverse engineering cellular networks
Nature Protocols. 2006. 1(2):662-671.
Wang K, Banerjee N, Margolin AA, Nemenman I, Califano A, 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 Katia, Liso Arcangelo, Tiacci Enrico, Benedetti Roberta, Pulsoni Alessandro, Foa Robin, Di Raimondo Francesco, Ambrosetti Achille, Califano Andrea, Klein Ulf, Dalla Favera Riccardo, and Falini Brunangelo
Gene Expression Profiling of Hairy Cell Leukemia Reveals a Phenotype Related to Memory B Cells with Altered Expression of Chemokine and Adhesion Receptors
Published 5 January 2004. doi:10.1084/jem.20031175
© Rockefeller University Press, 0022-1007 JEM, Volume 199, Number 1, 59-68
Katia Basso, Ulf Klein, Huifeng Niu, Gustavo A. Stolovitzky, Yuhai Tu, Andrea Califano, Giorgio Cattoretti, and Riccardo Dalla-Favera
Tracking CD40 signaling during germinal center development
Blood, 15 December 2004, Vol. 104, No. 13, pp. 4088-4096. Prepublished online as a Blood First Edition Paper on August 26, 2004; DOI 10.1182/blood-2003-12-4291.
Califano Andrea, and Liu Agatha H.
CASTOR: Clustering Algorithm for Sequence Taxonomical Organization and Relationships
Journal of Computational Biology,Feb 2003, Vol. 10, No. 1: 21-45
First Genetic Trust, Inc., 201 Rt. 17 North, Rutherford, NJ 07070
Küppers Ralf, Klein Ulf, Schwering Ines, Distler Verena, Bräuninger Andreas, Cattoretti Giorgio, Tu Yuhai, Stolovitzky Gustavo A., Califano Andrea, Hansmann Martin-Leo, and Dalla-Favera Riccardo
Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling
J Clin Invest. 2003 February 15; 111(4): 529–537.
doi: 10.1172/JCI200316624.
Copyright © 2003, American Society for Clinical Investigation
Klein Ulf, Tu Yuhai, Stolovitzky Gustavo A., Keller Jeffrey L., Haddad Jr. Joseph, Miljkovic Vladan, Cattoretti Giorgio, Califano Andrea, and Dalla-Favera Riccardo
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.
Klein U, Tu Y, Stolovitzky GA, Keller JL, Haddad Jr. H, Miljkovic V, Cattoretti G, Califano A, and Dalla-Favera R,
Gene expression dynamics during germinal center transit in B-cells,
Submitted to NYAS, 2002. (*senior authors, Dalla-Favera and Califano)
Margolin A, Nemenman I, Wiggins C, Stolovitzky G, Califano A
On the Reconstruction of Interaction Networks with Applications to Transcriptional Regulation, Neural Information Processing Systems
Workshop on New Problems and Methods in Computational Biology, Whistler, BC, Canada.
Basso K, Klein U, Niu H, Stolovitzky GA, Tu Y, Califano A, Cattoretti G, and Dalla-Favera R,
Tracking CD40 Signaling During Normal Germinal Center Development by Gene Expression Profiling,
Submitted to NYAS, 2002.
Buchanan A, Califano A, Kahn J, McPherson E, Robertson J, Brody B.
Pharmacogenetics: ethical issues and policy options.
Kennedy Inst Ethics J. 2002 Mar;12(1):1-15.
Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR.
Prediction of central nervous system embryonal tumour outcome based on gene expression.
Nature. 2002 Jan 24;415(6870):436-42.
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;19(11):1625-38.. (*senior authors, Dalla-Favera and Califano)
Califano A
Advances in Sequence Analysis
Current Opinion in Structural Biology. 2001. 11(3):330-3.
Liu A and Califano A,
Functional Classification of Proteins by pattern discovery and top-down clustering of primary sequences,
in IBM Systems Journal, special issue on Deep Computing for the Life Sciences, Volume 40, Number 2, 2001 40(2):379-393
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, Germain B, and Colville S
A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification
Lecture Notes in Computer Science. 1997 1351:32-39.
Germain RS, Califano A, and Colville S
Fingerprint Matching Using Transformation Parameter Clustering
IEEE Journal of Computational Science and Engineering. 1997 4(4):42-49.
Califano A, Kjeldsen R, and Bolle RM
Data- and model-driven multiresolution processing
Journal of Computer Vision and Image Understanding. 1996. 63(1):27-49.