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1.

Validation and refinement of gene-regulatory pathways on a network of physical interactions.

Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T.

Genome Biol. 2005;6(7):R62. Epub 2005 Jul 1.

PMID:
15998451
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Computational and experimental approaches for modeling gene regulatory networks.

Goutsias J, Lee NH.

Curr Pharm Des. 2007;13(14):1415-36. Review.

PMID:
17504165
[PubMed - indexed for MEDLINE]
3.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
[PubMed - indexed for MEDLINE]
4.

Gene networks: how to put the function in genomics.

Brazhnik P, de la Fuente A, Mendes P.

Trends Biotechnol. 2002 Nov;20(11):467-72. Review.

PMID:
12413821
[PubMed - indexed for MEDLINE]
5.

Refining regulatory networks through phylogenetic transfer of information.

Zhang X, Moret BM.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1032-45. doi: 10.1109/TCBB.2012.62.

PMID:
22547434
[PubMed - indexed for MEDLINE]
6.

EXAMINE: a computational approach to reconstructing gene regulatory networks.

Deng X, Geng H, Ali H.

Biosystems. 2005 Aug;81(2):125-36.

PMID:
15951103
[PubMed - indexed for MEDLINE]
7.
8.

Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments.

Gong Y, Zhang Z.

Ann N Y Acad Sci. 2007 Dec;1115:267-85. Epub 2007 Oct 9.

PMID:
17925355
[PubMed - indexed for MEDLINE]
9.

Genome-scale network analysis of imprinted human metabolic genes.

Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO.

Epigenetics. 2009 Jan;4(1):43-6. Epub 2009 Jan 31. Review.

PMID:
19218833
[PubMed - indexed for MEDLINE]
Free Article
10.

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.

Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L.

Science. 2001 May 4;292(5518):929-34.

PMID:
11340206
[PubMed - indexed for MEDLINE]
Free Article
11.

Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations.

Hallén K, Björkegren J, Tegnér J.

BMC Bioinformatics. 2006 Feb 2;7:51.

PMID:
16451737
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm.

Wang M, Augusto Benedito V, Xuechun Zhao P, Udvardi M.

Mol Biosyst. 2010 Jun;6(6):988-98. doi: 10.1039/b917571g. Epub 2010 Feb 19.

PMID:
20485743
[PubMed - indexed for MEDLINE]
13.

Chemical biology on PINs and NeeDLes.

Campbell-Valois FX, Michnick S.

Curr Opin Chem Biol. 2005 Feb;9(1):31-7. Review.

PMID:
15701450
[PubMed - indexed for MEDLINE]
14.

A predictive model of the oxygen and heme regulatory network in yeast.

Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.

PLoS Comput Biol. 2008 Nov;4(11):e1000224. doi: 10.1371/journal.pcbi.1000224. Epub 2008 Nov 14.

PMID:
19008939
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Matrix formalism to describe functional states of transcriptional regulatory systems.

Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO.

PLoS Comput Biol. 2006 Aug 11;2(8):e101.

PMID:
16895435
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Large-scale discovery and validation of functional elements in the human genome.

Bernstein BE, Kellis M.

Genome Biol. 2005;6(3):312. Epub 2005 Mar 1.

PMID:
15774039
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genome-wide atlas of gene expression in the adult mouse brain.

Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR.

Nature. 2007 Jan 11;445(7124):168-76. Epub 2006 Dec 6.

PMID:
17151600
[PubMed - indexed for MEDLINE]
18.

A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.

Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP.

Cell. 2009 Apr 3;137(1):172-81. doi: 10.1016/j.cell.2009.01.055. Epub 2009 Mar 26.

PMID:
19327819
[PubMed - indexed for MEDLINE]
Free Article
19.

Inferring regulatory networks.

Li H, Xuan J, Wang Y, Zhan M.

Front Biosci. 2008 Jan 1;13:263-75. Review.

PMID:
17981545
[PubMed - indexed for MEDLINE]
20.

Reconstructing pathways in large genetic networks from genetic perturbations.

Wagner A.

J Comput Biol. 2004;11(1):53-60.

PMID:
15072688
[PubMed - indexed for MEDLINE]

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