A parallel implementation of the network identification by multiple regression (NIR) algorithm to reverse-engineer regulatory gene networks

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Gregoretti, Francesco ^a   Belcastro, Vincenzo ^b   di Bernardo, Diego ^b   Oliva, Gennaro ^a  

^a High Performance Computing and Networking Institute (ICAR)   (Italy)

^b TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOMEDICINE; COMPUTER PROGRAM; DATA ANALYSIS; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC ENGINEERING; MATHEMATICAL ANALYSIS; MICROARRAY ANALYSIS; REGULATOR GENE; ALGORITHM; BIOLOGY; DNA MICROARRAY; GENE REGULATORY NETWORK; HUMAN; METHODOLOGY; REGRESSION ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGRESSION ANALYSIS;

EID: 77956321735     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010179     Document Type: Article

References (10)

1. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 95: 14863-14868.
2. Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2004) Advances to bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20: 3594-3603.
3. Heckerman D (1995) A tutorial on learning with bayesian networks. Technical report, Microsoft Research, Redmond, Washington. URL http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.56.1431.
4. Butte AJ, Kohane IS (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. pp 418-429.
5. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7 Suppl 1: S7.
6. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3: 78.
7. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
8. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3.
9. Newman MEJ (2003) The structure and function of complex networks. SIAM Review 45: 167-256.
10. Anderson E, Bai Z, Bischof C, Demmel J, Dongarra J, et al. (1992) LAPACK's user's guide. Philadelphia, PA, USA: Society for Industrial and Applied Mathematics.