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• FAQ
  Floratos A, Smith K, Ji Z, Watkinson J, Califano A. (2010). geWorkbench: an open source platform for integrative genomics.
  8 KB (1,336 words) - 18:39, 23 January 2015
• Pattern Discovery
  Regular Discovery is based on the algorithm SPLASH (Califano, A., 2000); it generates a list of all regular expression patterns (motifs) Califano, A. (2000). SPLASH: structural pattern localization analysis by sequential
  15 KB (2,347 words) - 21:39, 26 January 2015
• ARACNe
  * Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet 2 ...olin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R and Califano A, (2006a) ARACNE: An Algorithm for the Reconstruction of Gene Regulatory
  29 KB (4,490 words) - 17:26, 30 January 2015
• Cellular Networks KnowledgeBase
  ...ontext-specific regulatory interactomes developed in the lab of Dr. Andrea Califano at Columbia University.
  25 KB (3,894 words) - 17:36, 17 March 2015
• MINDy
  # Margolin, A., Wang, K., Lim, W.K., Kustagi, M., Nemenman, I., and Califano, A. (2006) Reverse Engineering Cellular Networks. Nature Protocols 1(2):662 ...dari 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 t
  26 KB (4,164 words) - 18:52, 22 January 2014
• Tutorial - temp
  Margolin, A., Wang, K., Lim, W.K., Kustagi, M., Nemenman, I., and Califano, A. Reverse Engineering Cellular Networks. Nature Protocols (2006), Vol 1,
  15 KB (2,337 words) - 15:00, 15 July 2009
• Master Regulator Analysis
  * Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005). Reverse engineering of regulatory networks in human B cells. Nat ...Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A (2010) The transcriptional network for mesenchymal transfor
  10 KB (1,558 words) - 17:47, 31 July 2014
• Release Descriptions
  ...e includes a new version of ARACNe, called ARACNe2, from the lab of Andrea Califano at Columbia University. The new version adds the option to preprocess the
  34 KB (5,033 words) - 11:27, 22 December 2016
• CNKB Data
  |Califano lab |Califano lab
  10 KB (1,253 words) - 18:06, 11 February 2015
• IDEA
  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 molecul
  2 KB (352 words) - 14:56, 25 April 2014
• MARINa
  ...ial 2-tailed version of GSEA is used, as described in Lim WK, Lyashenko E, Califano A (2009). * Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005). Reverse engineering of regulatory networks in human B cells. Nat
  23 KB (3,707 words) - 18:45, 6 March 2015
• MRA-FET
  * Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005). Reverse engineering of regulatory networks in human B cells. Nat ...Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A (2010) The transcriptional network for mesenchymal transfor
  19 KB (3,030 words) - 16:38, 9 March 2015
• CeRNA Query
  ...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 re
  2 KB (365 words) - 13:25, 22 May 2014
• PreviousReleases
  ...e includes a new version of ARACNe, called ARACNe2, from the lab of Andrea Califano at Columbia University. The new version adds the option to preprocess the
  27 KB (3,966 words) - 17:27, 15 July 2013
• Cupid
  ...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 re
  7 KB (967 words) - 16:43, 13 January 2014
• Viper Analysis
  Mariano Alvarez Yao Shen, B. Belinda Ding, B. Hilda Ye and Andrea Califano, manuscript in preparation.
  4 KB (603 words) - 17:34, 10 February 2015
• VIPER License
  ...VIPER software computer program developed in the laboratory of Dr. Andrea Califano and supplied to You pursuant to this Agreement.
  10 KB (1,518 words) - 15:09, 22 November 2013
• DeMAND License
  ...DeMAND software computer program developed in the laboratory of Dr. Andrea Califano and supplied to You pursuant to this Agreement.
  10 KB (1,518 words) - 15:14, 22 November 2013
• DeMAND
  ...M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A (2010) A human B-cell interactome identifies MYB and FOXM1 as master reg ...nez M, López G, Mattioli M, Realubit R, Karan C, Stockwell BR, Bansal M, Califano A (2015) Elucidating Compound Mechanism of Action by Network Perturbation A
  5 KB (726 words) - 15:09, 29 July 2015
• Cite
  Floratos A, Smith K, Ji Z, Watkinson J, Califano A. (2010). geWorkbench: an open source platform for integrative genomics.
  601 bytes (83 words) - 12:24, 16 September 2014

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