A citation-based method for searching scientific literature

Uri Alon. Nat Rev Genet 2007
Times Cited: 1556







List of co-cited articles
475 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Structure and function of the feed-forward loop network motif.
S Mangan, U Alon. Proc Natl Acad Sci U S A 2003
995
23

Network motifs: simple building blocks of complex networks.
R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii, U Alon. Science 2002
22

Network motifs in the transcriptional regulation network of Escherichia coli.
Shai S Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon. Nat Genet 2002
15


Defining network topologies that can achieve biochemical adaptation.
Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell A Lim, Chao Tang. Cell 2009
491
11


Stochastic gene expression in a single cell.
Michael B Elowitz, Arnold J Levine, Eric D Siggia, Peter S Swain. Science 2002
9

Construction of a genetic toggle switch in Escherichia coli.
T S Gardner, C R Cantor, J J Collins. Nature 2000
8

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.
John J Tyson, Katherine C Chen, Bela Novak. Curr Opin Cell Biol 2003
889
8

The incoherent feedforward loop can provide fold-change detection in gene regulation.
Lea Goentoro, Oren Shoval, Marc W Kirschner, Uri Alon. Mol Cell 2009
250
7



Network biology: understanding the cell's functional organization.
Albert-László Barabási, Zoltán N Oltvai. Nat Rev Genet 2004
6



Information transduction capacity of noisy biochemical signaling networks.
Raymond Cheong, Alex Rhee, Chiaochun Joanne Wang, Ilya Nemenman, Andre Levchenko. Science 2011
262
6

Transcriptional regulatory networks in Saccharomyces cerevisiae.
Tong Ihn Lee, Nicola J Rinaldi, François Robert, Duncan T Odom, Ziv Bar-Joseph, Georg K Gerber, Nancy M Hannett, Christopher T Harbison, Craig M Thompson, Itamar Simon,[...]. Science 2002
6

Superfamilies of evolved and designed networks.
Ron Milo, Shalev Itzkovitz, Nadav Kashtan, Reuven Levitt, Shai Shen-Orr, Inbal Ayzenshtat, Michal Sheffer, Uri Alon. Science 2004
494
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
5



Forcing cells to change lineages.
Thomas Graf, Tariq Enver. Nature 2009
594
5

A Polycomb-based switch underlying quantitative epigenetic memory.
Andrew Angel, Jie Song, Caroline Dean, Martin Howard. Nature 2011
266
4

Robust, tunable biological oscillations from interlinked positive and negative feedback loops.
Tony Yu-Chen Tsai, Yoon Sup Choi, Wenzhe Ma, Joseph R Pomerening, Chao Tang, James E Ferrell. Science 2008
396
4

A genomic regulatory network for development.
Eric H Davidson, Jonathan P Rast, Paola Oliveri, Andrew Ransick, Cristina Calestani, Chiou-Hwa Yuh, Takuya Minokawa, Gabriele Amore, Veronica Hinman, Cesar Arenas-Mena,[...]. Science 2002
912
4

A fast, robust and tunable synthetic gene oscillator.
Jesse Stricker, Scott Cookson, Matthew R Bennett, William H Mather, Lev S Tsimring, Jeff Hasty. Nature 2008
639
4

Community structure in social and biological networks.
M Girvan, M E J Newman. Proc Natl Acad Sci U S A 2002
4

Oscillations in NF-kappaB signaling control the dynamics of gene expression.
D E Nelson, A E C Ihekwaba, M Elliott, J R Johnson, C A Gibney, B E Foreman, G Nelson, V See, C A Horton, D G Spiller,[...]. Science 2004
834
4


p53 dynamics control cell fate.
Jeremy E Purvis, Kyle W Karhohs, Caroline Mock, Eric Batchelor, Alexander Loewer, Galit Lahav. Science 2012
450
4

Enhancement of cellular memory by reducing stochastic transitions.
Murat Acar, Attila Becskei, Alexander van Oudenaarden. Nature 2005
351
4

Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.
Sara Hooshangi, Stephan Thiberge, Ron Weiss. Proc Natl Acad Sci U S A 2005
319
4

Wisdom of crowds for robust gene network inference.
Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky. Nat Methods 2012
792
4

Bacterial persistence as a phenotypic switch.
Nathalie Q Balaban, Jack Merrin, Remy Chait, Lukasz Kowalik, Stanislas Leibler. Science 2004
4


Transcriptional regulation by the numbers: models.
Lacramioara Bintu, Nicolas E Buchler, Hernan G Garcia, Ulrich Gerland, Terence Hwa, Jané Kondev, Rob Phillips. Curr Opin Genet Dev 2005
448
4

Negative autoregulation speeds the response times of transcription networks.
Nitzan Rosenfeld, Michael B Elowitz, Uri Alon. J Mol Biol 2002
428
4

Spatiotemporal control of gene expression with pulse-generating networks.
Subhayu Basu, Rishabh Mehreja, Stephan Thiberge, Ming-Tang Chen, Ron Weiss. Proc Natl Acad Sci U S A 2004
269
4

Design principles of biochemical oscillators.
Béla Novák, John J Tyson. Nat Rev Mol Cell Biol 2008
556
4

Summing up the noise in gene networks.
Johan Paulsson. Nature 2004
758
4

Optimal signal processing in small stochastic biochemical networks.
Etay Ziv, Ilya Nemenman, Chris H Wiggins. PLoS One 2007
82
4

Systems biology: a brief overview.
Hiroaki Kitano. Science 2002
4

Functional motifs in biochemical reaction networks.
John J Tyson, Béla Novák. Annu Rev Phys Chem 2010
174
4

The incoherent feed-forward loop can generate non-monotonic input functions for genes.
Shai Kaplan, Anat Bren, Erez Dekel, Uri Alon. Mol Syst Biol 2008
109
4



Systems biology of stem cell fate and cellular reprogramming.
Ben D Macarthur, Avi Ma'ayan, Ihor R Lemischka. Nat Rev Mol Cell Biol 2009
227
3

Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.
Ruben Perez-Carrasco, Chris P Barnes, Yolanda Schaerli, Mark Isalan, James Briscoe, Karen M Page. Cell Syst 2018
35
8

Teleonomic mechanisms in cellular metabolism, growth, and differentiation.
J MONOD, F JACOB. Cold Spring Harb Symp Quant Biol 1961
685
3


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.