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Page 1
The Cyni framework for network inference in Cytoscape.
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. Guitart-Pla O, et al. Among authors: califano a. Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18. Bioinformatics. 2015. PMID: 25527096 Free PMC article.
Reverse engineering cellular networks.
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Margolin AA, et al. Among authors: califano a. Nat Protoc. 2006;1(2):662-71. doi: 10.1038/nprot.2006.106. Nat Protoc. 2006. PMID: 17406294
geWorkbench: an open source platform for integrative genomics.
Floratos A, Smith K, Ji Z, Watkinson J, Califano A. Floratos A, et al. Among authors: califano a. Bioinformatics. 2010 Jul 15;26(14):1779-80. doi: 10.1093/bioinformatics/btq282. Epub 2010 May 28. Bioinformatics. 2010. PMID: 20511363 Free PMC article.
Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.
Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C, Villagrasa-Gonzalez P, Viale A, Korkola JE, Houldsworth J, Feldman DR, Bosl GJ, Califano A, Chaganti RS. Kushwaha R, et al. Among authors: califano a. Stem Cells. 2015 Feb;33(2):367-77. doi: 10.1002/stem.1870. Stem Cells. 2015. PMID: 25336442 Free PMC article.
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Lachmann A, Giorgi FM, Lopez G, Califano A. Lachmann A, et al. Among authors: califano a. Bioinformatics. 2016 Jul 15;32(14):2233-5. doi: 10.1093/bioinformatics/btw216. Epub 2016 Apr 23. Bioinformatics. 2016. PMID: 27153652 Free PMC article.
Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest computational resources to build complex regulatory networks from hundreds of gene expression profiles. AVAILABILITY AND IMPLEMENTATION: A …
Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest c …
360 results