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SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences

https://doi.org/10.1371/journal.pone.0151740

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00439-013-1413-1openalex-snapshot

The grammar of transcriptional regulation

inferredcites →https://doi.org/10.1016/j.cell.2014.11.041openalex-snapshot

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

inferredcites →https://doi.org/10.1016/j.celrep.2013.03.014openalex-snapshot

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

inferredcites →https://doi.org/10.1016/j.celrep.2015.08.021openalex-snapshot

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

inferredcites →https://doi.org/10.1016/j.cub.2010.07.043openalex-snapshot

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

inferredcites →https://doi.org/10.1016/j.devcel.2009.12.026openalex-snapshot

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

inferredcites →https://doi.org/10.1016/j.tibs.2014.07.002openalex-snapshot

Absence of a simple code: how transcription factors read the genome

inferredcites →https://doi.org/10.1038/nmeth.2918openalex-snapshot

Large-scale de novo DNA synthesis: technologies and applications

inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot

Transcription factors: from enhancer binding to developmental control

inferredcites →https://doi.org/10.1073/pnas.1422023112openalex-snapshot

Quantitative modeling of transcription factor binding specificities using DNA shape

inferredcites →https://doi.org/10.1073/pnas.142291299openalex-snapshot

Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex

inferredcites →https://doi.org/10.1093/nar/10.9.2997openalex-snapshot

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites in E. coli

inferredcites →https://doi.org/10.1186/1471-2105-10-442openalex-snapshot

G+C content dominates intrinsic nucleosome occupancy

inferredcites →https://doi.org/10.1242/dev.010744openalex-snapshot

A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in theDrosophilaembryo

inferredcites →https://doi.org/10.1371/journal.pgen.1004060openalex-snapshot

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

inferredcites →https://doi.org/10.3389/fmicb.2014.00735openalex-snapshot

oriC-encoded instructions for the initiation of bacterial chromosome replication

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Defining Kinetic Roles of Transcriptional Activators in the Early Drosophila Embryo

inferred← citeshttps://doi.org/10.1007/978-1-0716-4220-7_7openalex-snapshot

Use of a Golden Gate Plasmid Set Enabling Scarless MoClo-Compatible Transcription Unit Assembly

inferred← citeshttps://doi.org/10.1016/j.celrep.2019.01.115openalex-snapshot

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

inferred← citeshttps://doi.org/10.1016/j.cels.2022.12.008openalex-snapshot

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

inferred← citeshttps://doi.org/10.1016/j.cels.2023.03.006openalex-snapshot

Transcriptional activators in the early Drosophila embryo perform different kinetic roles

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Quantum Dot Encoding for In-Solution Single-Molecule Biomarker Counting in Metastatic Prostate Cancer

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Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements

inferred← citeshttps://doi.org/10.1038/s41467-024-53539-0openalex-snapshot

Optogenetic dissection of transcriptional repression in a multicellular organism

inferred← citeshttps://doi.org/10.1038/s41467-026-72618-yopenalex-snapshot

Enhancer placement impacts transcriptional dynamics in Drosophila embryos

inferred← citeshttps://doi.org/10.1038/s41590-019-0449-3openalex-snapshot

An Nfil3–Zeb2–Id2 pathway imposes Irf8 enhancer switching during cDC1 development

inferred← citeshttps://doi.org/10.1039/c5ib00321kopenalex-snapshot

The appeasement of Doug: a synthetic approach to enhancer biology

inferred← citeshttps://doi.org/10.1073/pnas.2211203120openalex-snapshot

Competing constraints shape the nonequilibrium limits of cellular decision-making

inferred← citeshttps://doi.org/10.1093/synbio/ysae016openalex-snapshot

In - & Out-Cloning : plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly

inferred← citeshttps://doi.org/10.1101/2021.02.25.432925openalex-snapshot

Defining kinetic roles of transcriptional activators in the early Drosophila embryo

inferred← citeshttps://doi.org/10.1101/2021.07.10.451524openalex-snapshot

Minimal Synthetic Enhancers Reveal Control of the Probability of Transcriptional Engagement and its Timing by a Morphogen Gradient

inferred← citeshttps://doi.org/10.1101/335919openalex-snapshot

Multimodal transcriptional control of pattern formation in embryonic development

inferred← citeshttps://doi.org/10.1128/aem.00603-18openalex-snapshot

An Iterative, Synthetic Approach To Engineer a High-Performance PhoB-Specific Reporter

inferred← citeshttps://doi.org/10.48550/arxiv.2108.05848openalex-snapshot

Eliminating unwanted patterns with minimal interference

inferred← citeshttps://doi.org/10.7554/elife.41266openalex-snapshot

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

inferred← citeshttps://doi.org/10.7554/elife.73395openalex-snapshot

Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer

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