Combinatorial binding predicts spatio-temporal cis-regulatory activity

By R. Zinzen, Charles Girardot, J. Gagneur, Martina Braun, E. Furlong. Nature, 2009

417 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2f52e8c7c338ed5bc1083e99ad19a9f8830425c5

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Citations in the corpus

Gaussian Process Regression Networks (2011, methodology): “Tomancak et al. (2002) measured gene expression levels every hour for 12 hours during Drosophila embryogenesis; they then repeated this experiment for an independent replica (a second independent time series).”
A computational pipeline for comparative ChIP-seq analyses (2011, background): “The focus of many current ChIP-seq studies is the comparison of transcription factor binding profiles across different conditions such as different developmental time points 5,6 , cell types (e.g., within one cell lineage 7,8 ) or closely related species 9,10 .”
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development (2011, methodology): “To map the occupancy patterns of specific regulators, chromatin immunoprecipitation (ChIP) has been applied to over 20 developmental transcription factors and RNA polymerase in the blastoderm embryo and, for several factors, at later stages of embryogenesis [30-36].”
Functional and mechanistic diversity of distal transcription enhancers (2011, positive): “Themost accurate predictions for enhancer activity to date are derived from combinatorial analysis of the binding of multiple transcription factors across the genome in Drosophila (Zinzen et al., 2009).”
Genome-scale functional characterization of Drosophila developmental enhancers in vivo (2014, background): “Animal development depends on differential gene expression gov-ernedbygenomicregulatoryelementscalledenhancers 1,9 ,whicharebeing studied extensively 2,3,8,10,11 .”
Computationally Efficient Convolved Multiple Output Gaussian Processes (2011, background): “We compare the performance of the intrinsic coregionalization model (Section 2.1.1) and the convolved GPs for two indepe nt time series or replicas of 12 time points collected hourly throughout Drosophila embryogenesis in wild-type embryos (Tomancak et al., 2002).”
Transcriptional enhancers: from properties to genome-wide predictions (2014, methodology): “Approaches for finding over-represented motifs can be applied to any set of sequences that share some functional or biochemical similarity, for example, regions that act as enhancers in the same tissue and regions bound by the same transcription factor in vivo 35,36,120 .”