Andrea Califano, Columbia University, USA

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

Lezione 1: Dissecting and interrogating the transcriptional logic of the cell: Elucidating human disease drivers and associated regulatory mechanisms.

  1. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. 2005. Reverse engineering of regulatory networks in human B cells. Nat Genet 37: 382-90
  2. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. 2006. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 Suppl 1: S7
  3. Zhao X, D DA, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. 2009. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell 17: 210-21
  4. 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. 2010. The transcriptional network for mesenchymal transformation of brain tumours. Nature 463: 318-25

Lezione 2: Dissecting and interrogating the post-transcriptional and post-translational logic of the cell: from competitive endogenous RNAs to signal transduction networks.

  1. 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. 2009. Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature 459: 717-21
  2. 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. 2009. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol 27: 829-39
  3. Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. 2011. An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma. Cell 147: 307
  4. 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. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490: 556-60

Lezione 3: Integrative analysis of cellular networks to elucidate drug-related phenotypes: drug sensitivity, synergy, and mechanism of action.

  1. Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A. 2008. A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 4: 169
  2. 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 A. 2013. Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell