Evidence map›Paper›PMID 42239281›Full record

ArticlebioRxiv : the preprint server for biology2026

Informational blueprints reveal condition-dependent gene regulatory architectures.

Doruk Efe Gökmen, Rosalind Wenshan Pan, Tom Röschinger, Stephen Quake, Hernan G Garcia, Rob Phillips, Vincenzo Vitelli

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

7 authors.

Doruk Efe GökmenNSF-Simons National Institute for Theory and Mathematics in Biology, Chicago, IL 60611, USA.ORCID 0000-0002-5536-1941
Rosalind Wenshan PanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Tom RöschingerDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Stephen QuakeDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Hernan G GarciaDepartments of Molecular & Cell Biology and of Physics, Biophysics Graduate Group, Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA.ORCID 0000-0002-5212-3649
Rob PhillipsDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Vincenzo VitelliJames Franck Institute, The University of Chicago, Chicago, IL 60637, USA.

Funding

The Principles of Regulatory, Conformational and Evolutionary AdaptationR35GM118043 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI ROB PHILLIPS · 2016 to 2026
$7.9M
NIH Director's Pioneer Award (RMI)DP1OD000217 · OD · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI PHILLIPS, ROB · 2004 to 2008
$4.0M
Physical Biology of Transcriptional Control in Embryonic DevelopmentR35GM158200 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Hernan Gustavo Garcia · 2025 to 2026
$847k
NIGMS NIH HHS R35 GM118043NIGMS NIH HHS R35 GM158200NIH HHS DP1 OD000217
6 · The paper itself

Abstract

While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that identifies where regulatory proteins, known as transcription factors (TFs), bind. Here, we extract these binding sites by distilling sequences of nucleotide letters into collective coordinates (hyperletters) representing the binding sites that are active under specific environmental conditions. Going beyond local information footprints between individual bases and expression levels, our

Identifiers

PMID42239281
PMCPMC13228646

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.