Nonnegative network component analysis by linear programming for gene regulatory network reconstruction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5441, Issue , 2009, Pages 395-402

  Chang, Chunqi ^a   Ding, Zhi ^b   Hung, Yeung Sam ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b University of California Davis   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONVENTIONAL METHODS; GENE EXPRESSION MICROARRAY; GENE REGULATORY NETWORKS; LINEAR PROGRAMMING PROBLEM; MICROARRAY DATA; MIXING MATRIX; NETWORK COMPONENT ANALYSIS; NOISE ROBUSTNESS; NON-NEGATIVITY; ON TIME; SIMULATION RESULT; SOURCE SEPARATION; SPECTROSCOPY DATA; STRUCTURAL INFORMATION; SYSTEMS BIOLOGY; YEAST CELL CYCLES;

APARTMENT HOUSES; DYNAMIC PROGRAMMING; GENE EXPRESSION; HEMODYNAMICS; INDEPENDENT COMPONENT ANALYSIS; LINEARIZATION; NETWORK COMPONENTS; SEPARATION; SIGNAL ANALYSIS;

BLIND SOURCE SEPARATION;

EID: 67149094741     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-00599-2_50     Document Type: Conference Paper

References (16)

1. Savageau, M.A.: Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, Reading (1976)
2. Liebermeister, W.: Linear modes of gene expression determined by independent component analysis. Bioinformatics 18(1), 51-60 (2002)
3. Lee, S.I., Batzoglou, S.: Application of independent component analysis to microar- rays. Genome Biology 4(11), 76 (2003)
4. Abrard, F., Deville, Y.: Blind separation of dependent sources using the "time- frequency ratio of mixtures" approach. In: Proceedings of Seventh International Symposium on Signal Processing and Its Applications, pp. 81-84 (July 2003)
5. Chang, C.Q., Ren, J., Fung, P., Hung, Y., Shen, J., Chan, F.: Novel sparse component analysis approach to free radical EPR spectra decomposition. Journal of Magnetic Resonance 175(2), 242-255 (2005)
6. Liao, J.C., Boscolo, R., Yang, Y.L., Tran, L.M., Sabatti, C., Roychowdhury, V.P.: Network component analysis: Reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences of the United States of America 100(26), 15522-15527 (2003)
7. Tran, L.M., Brynildsen, M.P., Kao, K.C., Suen, J.K., Liao, J.C.: gnca: A framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation. Metabolic Engineering 7, 128-141 (2005)
8. Chang, C.Q., Ding, Z., Hung, Y.S., Fung, P.C.W.: Fast network component analysis for gene regulation networks. In: Proc. 2007 IEEE International Workshop on Machine Learning for Signal Processing, Thesaloniki, Greece (2007)
9. Chang, C.Q., Ding, Z., Hung, Y.S., Fung, P.C.W.: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data. Bioinformatics 24, 1349 (2008)
10. Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman &Hall/CRC (2007)
11. Golub, G.H., van Loan, C.F.: Matrix Computation, 3rd edn. The Johns Hopkins University Press (1996)
12. Dantzig, G.: Linear Programming and Extensions. Princeton Univ. Pr., Princeton (1963)
13. Luenberger, D.: Introduction to Linear and Nonlinear Programming. AddisonWesley Pub. Co., Reading (1973)
14. GNU: GLPK (GNU Linear Programming Kit) [web page and software] (2008), http://www.gnu.org/software/glpk/glpk.html
15. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botsein, D., Futcher, B.: Comprehensive identification of cell cycle- regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9(12), 3273-3297 (1998)
16. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gilford, D.K., Young, R.A.: Transcriptional regulatory networks in saccharomyces cerevisiae. Science 298(5594), 799-804 (2002)