ReviewProceedings of the National Academy of Sciences of the United States of America2005
Logic functions of the genomic cis-regulatory code.
Review in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Synthesizing Mechanistic Hypotheses from Single-Cell Omics via Discretized Feature Attribution and Empirical Language Model Grounding.bioRxiv : the preprint server for biology · 2026Article
- Lineage-Selective Dependencies in Pediatric Cancers.Cold Spring Harbor perspectives in medicine · 2025Review
- Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee.Molecular biology and evolution · 2024Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- ACell genomics · 2022Article
- Seven myths of how transcription factors read the cis-regulatory code.Current opinion in systems biology · 2020Article
- Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map.Journal of the Royal Society, Interface · 2020Article
- Network architecture and regulatory logic in neural crest development.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Modeling somatic computation with non-neural bioelectric networks.Scientific reports · 2019Article
- How Does the Regulatory Genome Work?Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the GenomicJournal of computational biology : a journal of computational molecular cell biology · 2019Article
- Encounters across networks: Windows into principles of genomic regulation.Marine genomics · 2019Article
- An integrative method to decode regulatory logics in gene transcription.Nature communications · 2017Article
- Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence.Rice (New York, N.Y.) · 2016Article
- The spatiotemporal order of signaling events unveils the logic of development signaling.Bioinformatics (Oxford, England) · 2016Article
- Eric Davidson: Steps to a gene regulatory network for development.Developmental biology · 2016Article
- Mechanical stretch upregulates proteins involved in Ca2+ sensitization in urinary bladder smooth muscle hypertrophy.American journal of physiology. Cell physiology · 2014Article
- Identifying transcription factor complexes and their roles.Bioinformatics (Oxford, England) · 2014Article
- bHLH05 is an interaction partner of MYB51 and a novel regulator of glucosinolate biosynthesis in Arabidopsis.Plant physiology · 2014Article
- Quantitative modeling of a gene's expression from its intergenic sequence.PLoS computational biology · 2014Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
cis-Regulatory modules that control developmental gene expression process the regulatory inputs provided by the transcription factors for which they contain specific target sites. A prominent class of cis-regulatory processing functions can be modeled as logic operations. Many of these are combinatorial because they are mediated by multiple sites, although others are unitary. In this work, we illustrate the repertoire of cis-regulatory logic operations, as an approach toward a functional interpretation of the genomic regulatory code.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.