Network motifs publications:

General:

• S Shen-Orr, R Milo, S Mangan & U Alon,
  Network motifs in the transcriptional regulation network of Escherichia coli.
  Nature Genetics, 31:64-68 (2002). Pdf.
• R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii & U Alon,
  Network Motifs: Simple Building Blocks of Complex Networks
  Science, 298:824-827 (2002). Pdf.
• R Milo, S Itzkovitz, N Kashtan, R Levitt, S Shen-Orr, I Ayzenshtat, M Sheffer & U Alon,
  Superfamilies of designed and evolved networks
  Science, 303:1538-42 (2004). Pdf.
• U Alon,
  (Viewpoint) Biological Networks: The Tinkerer as an Engineer.
  Science, 301:1866-1867 (2003). Pdf.

Algorithms, Formula and Concepts:

• S Itzkovitz, R Milo, N Kastan, G Ziv & U Alon,
  Subgraphs in random networks
  Phys Rev E 68, 026127 (2003). Pdf.
• N. Kashtan, S. Itzkovitz, R. Milo, U. Alon,
  Topological Generalizations of network motifs.
  Phys Rev E 70, 031909 (2004).Pdf.
• N. Kashtan, S. Itzkovitz, R. Milo, U. Alon,
  Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs.
  Bioinformatics. 2004 Jul 22;20(11):1746-58. Pdf.
• Shalev Itzkovitz, Reuven Levitt, Nadav Kashtan, Ron Milo, Michael Itzkovitz, Uri Alon,
  Coarse-Graining and Self-Dissimilarity of Complex Networks.
  Phys Rev E 71, 016127 (2005). Pdf.
• Shalev Itzkovitz and Uri Alon,
  Subgraphs and network motifs in geometric networks.
  Phys Rev E 71, 026117 (2005). Pdf.
• E. Yeger-Lotem, S. Sattath, N. Kashtan, S. Itzkovitz, R. Milo, R. Pinter, U. Alon, H. Margalit
  Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction.
  PNAS, 2004 Apr 20 (2004). Pdf.
• R. Milo, N. Kashtan, S. Itzkovitz, M. E. J. Newman & U. Alon,
  Uniform generation of random graphs with arbitrary degree sequences
  cond-mat/0312028 (2003). Pdf.

Experiments and Theory on the Feed-Forward Loop Motif:

• S. Mangan, S. Itzkovitz, A. Zaslaver and U. Alon,
  The Incoherent Feed-forward Loop Accelerates the Response-time of the gal System of Escherichia coli.
  JMB, Vol 356 pp 1073-81 (2006). Pdf.
• S Mangan & U Alon,
  Structure and function of the feed-forward loop network motif.
  PNAS, 100:11980-11985 (2003). Pdf.
• S Mangan, A Zaslaver and U Alon,
  The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks.
  JMB, Vol 334/2 pp 197-204 (2003). Pdf.
• Shiraz Kalir and Uri Alon,
  Using a Quantitative Blueprint to Reprogram the Dynamics of the Flagella Gene Network
  Cell, 117:713–720, (2004). Pdf.
• See also cover page: URL.
• See also Preview article: Pdf.
• Shiraz Kalir, Shmoolik Mangan and Uri Alon,
  A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
  Mol Syst Biol, msb4100010-E1-msb4100010-E6, (2005). Pdf.

Experiments and Theory on the Single Input Module Motif:

• M Ronen, R Rosenberg, B Shraiman & U Alon,
  Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics.
  PNAS, 99:10555–10560 (2002). Pdf.
• See also JCB news: Pdf.
• Alon Zaslaver, Avi E Mayo, Revital Rosenberg, Pnina Bashkin, Hila Sberro, Miri Tsalyuk, Michael G Surette & Uri Alon,
  Just- in- time transcription program in metabolic pathways
  Nature Genetics 36, 486 - 491 (2004). Pdf.

Experiments and Theory on Negative Autoregulation Motif:

• N Rosenfeld, M Elowitz & U Alon,
  Negative Autoregulation Speeds the Response Times of Transcription Networks
  JMB, 323:785-793 (2002). Pdf.

Network motifs in developmental networks:

• Patrick Eichenberger1, Masaya Fujita1, Shane T. Jensen, Erin M. Conlon, David Z. Rudner, Stephanie T. Wang,Caitlin Ferguson, Koki Haga, Tsutomu Sato, Jun S. Liu & Richard Losick,
  The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis
  PLOS biology, 2:1664-1683 (2004). Pdf.