Evidence map›Paper›PMID 40631206›Full record

ArticlebioRxiv : the preprint server for biology2025

Systematic DNA nicking reveals the structural logic of protein recognition.

Yumi Minyi Yao, Michael P O'Hagan, Karn Onoon, Lihee Givon, Shelly Hamer-Rogotner, Raul Salinas, Naama Kessler, Orly Dym, Tanadet Pipatpolkai, Maria A Schumacher and 1 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

11 authors.

Yumi Minyi YaoDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.ORCID 0009-0002-7762-9731
Michael P O'HaganDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.ORCID 0000-0003-4180-3144
Karn OnoonDepartment of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
Lihee GivonDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Shelly Hamer-RogotnerDepartment of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel.
Raul SalinasDepartment of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.ORCID 0000-0001-9011-683X
Naama KesslerDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
Orly DymDepartment of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel.
Tanadet PipatpolkaiSchool of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore.ORCID 0000-0001-5396-4784
Maria A SchumacherDepartment of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.ORCID 0000-0002-5264-1120
Ariel AfekDepartment of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.ORCID 0000-0001-8584-9879

Funding

User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Gregory L Hura · 2017 to 2026
$28.6M
Deciphering fundamental biological processes involving protein-nucleic acid interactions at the molecular levelR35GM130290 · NIGMS · DUKE UNIVERSITY · PI Maria Schumacher · 2019 to 2026
$4.9M
A Fast Pixel-Array Pilatus 2M Detector for Automated Macromolecular Crystallography Data CollectionS10OD026941 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI ADAMS, PAUL DAVID · 2019 to 2019
$563k
NIGMS NIH HHS P30 GM124169NIGMS NIH HHS R35 GM130290NIH HHS S10 OD026941
6 · The paper itself

Abstract

Transcription factors (TFs) bind to specific genomic sites to regulate gene expression

Identifiers

PMID40631206
PMCPMC12236790

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.