BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing.

Arjun K Aditham, Tyler C Shimko, Polly M Fordyce

Abstract read

In one paragraph

Article in Methods in cell biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it

0cells of the map it votes in

3citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

Multiple overlapping binding sites determine transcription factor occupancy.Nature · 2025
Article
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.Nucleic acids research · 2023
Article
bioRxiv : the preprint server for biology · 2023
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Arjun K AdithamDepartment of Bioengineering, Stanford University, Stanford, CA, United States; Stanford ChEM-H, Stanford University, Stanford, CA, United States.

Tyler C ShimkoDepartment of Genetics, Stanford University, Stanford, CA, United States.

Polly M FordyceDepartment of Bioengineering, Stanford University, Stanford, CA, United States; Stanford ChEM-H, Stanford University, Stanford, CA, United States; Department of Genetics, Stanford University, Stanford, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States. Electronic address: pfordyce@stanford.edu.

Funding

Stanford Chem-H Chemistry/Biology Interface Predoctoral Training ProgramT32GM120007 · NIGMS · STANFORD UNIVERSITY · PI BERTOZZI, CAROLYN · 2016 to 2020

$1.2M

Using Microfluidic Affinity Analysis to Probe Transcriptional RegulationR00GM099848 · NIGMS · STANFORD UNIVERSITY · PI FORDYCE, POLLY MORRELL · 2015 to 2017

$747k

NIGMS NIH HHS R00 GM099848

6 · The paper itself

Abstract

Biophysical models of transcriptional regulation rely on energetic measurements of the binding affinities between transcription factors (TFs) and target DNA binding sites. Historically, assays capable of measuring TF-DNA binding affinities have been relatively low-throughput (measuring ~10

Indexed as

ThermodynamicsBiophysical PhenomenaHigh-Throughput Nucleotide SequencingMicrofluidic Analytical TechniquesSequence Analysis, DNABinding energy landscapeHigh-throughput sequencingMicrofluidicsProtein-DNA interactionsTranscription factor binding

Identifiers

PMID30473071

DOI10.1016/bs.mcb.2018.09.011

PMCPMC7531582

What OpenQuestion holds

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Registered trials

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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.