Andrea
Califano
Professor
1130 St. Nicholas Avenue, Herbert Irving Cancer Research Center, Room 912
New York
NY
10032
Email:
Office Phone:
(212) 851-5183
Fax:
(212) 851-4630
Website:
Short Research Description:
Study of gene regulatory and signaling networks in mammalian cellular contexts using computational methods.
Full Research Description:
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 and biochemical validation of gene regulatory and signaling networks in mammalian cellular contexts.
- The study of genetic regulatory modules that are disregulated in lymphoid malignancies and other human malignancies, using a systems biology approach.
- The dissection of regulatory networks necessary for pluripotency and lineage specific differentiation of human Stem Cells.
- The application of systems biology methods to the dissection of normal and pathologic phenotypes.
- The identification of cis-regulatory elements and modules in the non-coding genome of higher eukaryotes.
Representative Publications:
- Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM, Califano A.Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.,Cell 2014 PMID:25303533
- Bansal, M., J. Yang, C. Karan, M. P. Menden, J. C. Costello, H. Tang, G. Xiao, Y. Li, J. Allen, R. Zhong, B. Chen, M. Kim, T. Wang, L. Heiser, R. Realubit, M. Mattioli, M. Alvarez, Y. Shen, N.-D. community, D. Gallahan, D. Singer, J. Saez-Rodriguez, Y. Xie, G. Stolovitzky and A. Califano[ Predicting compound synergy from first principles, a crowdsourcing approach.],Nature Biotechnology 2014 PMID:in progress
- Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta K, Shen MM, Califano A, Abate-Shen C. 2014. Cross-species analysis of genome-wide regulatory networks identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell, in press
- Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RG, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. 2014. ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State. Cell Rep 6: 313-24
- Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P. 2014. The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected during Tumor Progression. Cancer Res 74: 1440-51
- Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. 2013. Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia. Cancer Cell 24: 766-76
- Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C.A molecular signature predictive of indolent prostate cancer., Sci Transl Med.2013 PMID:24027026
- Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Hussein S, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R. 2013. MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol14: 1084-92
- Wang ZA, Mitrofanova A, Bergren SK, Abate-Shen C, Cardiff RD, Califano A, Shen MM. Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity., Nat Cell Biol.2013 PMID: 23434823
- Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. Structure-based prediction of protein-protein interactions on a genome-wide scale, Nature 2012 Sep 30. PMID: 23023127
- Wang J, Kobayashi T, Floc'h N, Kinkade CW, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M, Califano A, Shen MM, Abate-Shen C. B-Raf Activation Cooperates with PTEN Loss to Drive c-Myc Expression in Advanced Prostate Cancer, Cancer Reserch 2012 Sep 15. PMID: 22836754
- Floch N, Kinkade CW, Kobayashi T, Aytes A, Lefebvre C, Mitrofanova A, Cardiff RD, Califano A, Shen MM, Abate-Shen C.Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. Cancer Res. 2012 Jul 19
- Martinez MR, Corradin A, Klein U, Alvarez MJ, Toffolo GM, di Camillo B, et al. Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.P Natl Acad Sci USA. 2012;109(7):2672-7.
- Della Gatta G, Palomero T, Perez-Garcia A, Ambesi-Impiombato A, Bansal M, Carpenter ZW, et al. Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med. 2012;18(3):436-U198
- Sumazin P, Yang XR, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, et al. An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma. Cell. 2011;147(2):370-81.
- Kruithof-de Julio M, Alvarez MJ, Galli A, Chu JH, Price SM, Califano A, et al. Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development. 2011;138(18):3885-95.
- De Keersmaecker K, Real PJ, Gatta GD, Palomero T, Sulis ML, Tosello V, Van Vlierberghe P, Barnes K, Castillo M, Sole X, Hadler M, Lenz J, Aplan PD, Kelliher M, Kee BL, Pandolfi PP, Kappes D, Gounari F, Petrie H, Van der Meulen J, Speleman F, Paietta E, Racevskis J, Wiernik PH, Rowe JM, Soulier J, Avran D, Cavé H, Dastugue N, Raimondi S, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. The TLX1 oncogene drives aneuploidy in T cell transformation, Nat Med. 2010 Oct 24. PMID: 20972433
- Cancer Target Discovery and Development Network, Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA. Towards patient-based cancer therapeutics, Nat Biotechnol. 2010 Sep;28(9):904-6. PMID: 20829823
- Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Mol Syst Biol. 2010 Jun 8;6:377. PMID: 20531406
- Floratos A, Smith K, Ji Z, Watkinson J, Califano A.geWorkbench: an open source platform for integrative genomics, Bioinformatics 2010 Jul 15;26(14):1779-80. Epub 2010 May 28. PMID: 20511363
- Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G, Dalla-Favera R. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia,Cancer Cell. 2010 Jan 19;17(1):28-40. PMID: 20060366
- Alvarez MJ, Sumazin P, Rajbhandari P, Califano A. Correlating measurements across samples improves accuracy of large-scale expression profile experiments, Genome Biol. 2009;10(12):R143. PMID: 20042104
- Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. The transcriptional network for mesenchymal transformation of brain tumours, Nature. 2010Jan 21;463(7279):318-25. PMID: 20032975
- Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim WK, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 2010 Feb 4;115(5):975-84.
- Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 2009 Sep;27(9):829-39.
- Zhao X, D' Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 2009Aug;17(2):210-21.
- Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11294-9
- Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J Jr, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity. 2009 May;30(5):744-52.
- Compagno M, Lim WK, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L.[http://www.ncbi.nlm.nih.gov/pubmed/19412164 Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 2009 Jun 4;459(7247):717-21.
- Lim WK, Lyashenko E, Califano A. Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. 2009:504-15.
- Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A. Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput. 2009:264-75.
- 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, Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9.
- Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol. 2008;4:169
- Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks Nature Protocols. 2006. 1(2):662-671.
- Sosinsky A, Honig B, Mann RS, Califano A. 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.
- 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 Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18261-6. Epub 2006 Nov 17. Erratum in: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):4240.
- Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.
- 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 200537, 382 - 390
- Katia Basso, Ulf Klein, Huifeng Niu, Gustavo A. Stolovitzky, Yuhai Tu, Andrea Califano, Giorgio Cattoretti, and Riccardo Dalla-FaveraTracking CD40 signaling during germinal center development Blood 2004 , 15 December 2004, Vol. 104, No. 13, pp. 4088-4096.
- 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 J. Exp. Med. 2004, Volume 199, Number 1, 59-68
- Liu A, Zhang X., Stolovitzky G, Califano A, and Firestein S,Motif-Based Construction of a Functional Map for Mammalian Olfactory Receptors, Genomics. 2003 May;81(5):443-56.
- 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 Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2639-44.
- 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.
- 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.
- Califano A, Stolovitzky S and Tu Y, Analysis of Gene Expression Microarrays for Phenotype Classification, Proc Int Conf Intell Syst Mol Biol. 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]. Proc Int Conf Intell Syst Mol Biol. 1993;1:56-64.