Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria

By Shiraz Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, Stanislas Leibler, Michael G. Surette, Uri Alon. Science, 2001

388 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f43e4d42be188f721b4d9cce59d044e4a47ae5a5

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Citations in the corpus

Recent Advances in Petroleum Microbiology (2003, background): “(300, 579) will allow this type of integrating study.”
Structure and evolution of transcriptional regulatory networks. (2004, neutral): “2004) and in the flagellar biogenesis pathway (Kalir et al. 2001).”
FANMOD: a tool for fast network motif detection (2006, methodology): “Both MFINDER and MAVISTO support the detection of network motifs consisting of up to eight vertices, but otherwise these tools have a different focus: MFINDER is a command-line tool that is concerned solely with the detection of network motifs whereas MAVISTO visualizes occurences of a motif in a ne”
Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking (2007, background): “The importance of network motifs as information-processing modules has been modeled theoretically [12,21] and verified experimentally [8,13,20,25].”
Measuring the activity of BioBrick promoters using an in vivo reference standard (2009, background): “Background fluorescence was determined at different ODs from the fluorescence of TOP10 cells without a GFP expressing vector [34].”
Network motifs in the transcriptional regulation network of Escherichia coli (2002, background): “This type of mechanism may explain the experimentally observed temporal program in the expression of flagella biosynthesis gene”
Transcriptional Regulation by the Numbers 1: Models (2004, neutral): “In a companion paper [1], these ideas are applied to several case studies which illustrate the use of the general formalism.”
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs (2004, background): “, 2002) and experimentally (Kalir et al., 2001; Ronen et al., 2002; Zaslaver et al., 2004) to generate temporal programs of expression.”
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. (2003, methodology): “Promoter activity was measured by means of an automated multiwell fluorimeter from cultures of strains bearing the reporter plasmids.(18,19) Both green fluorescent protein (GFP) fluorescence and optical absorbance (A600 nm) were measured at a very high temporal resolution (about once per minute).”
What is Systems Biology? (2010, background): “…example would be a comprehensive assessment of transcript diversity to identify simple design principles implementing speciﬁ c regulatory functions in a complex cellular network, such as Kalir et al. performed for the ﬂ agellar system of Escherichia coli (Kalir et al., 2001; Kalir and Alon, 2004).”
Negative autoregulation speeds the response times of transcription networks. (2002, methodology): “5 second, CW lamp energy 2482 units), and shaking (2 mm double-orbital, normal speed, 203 seconds).(24) Once every three repeats the shaking was replaced by automated injection of 7 ml double-distilled water into each well to counteract evaporation.”