Evidence map›Paper›PMID 39975366›Full record

ArticlebioRxiv : the preprint server for biology2025

CiFi: Accurate long-read chromatin conformation capture with low-input requirements.

Sean P McGinty, Gulhan Kaya, Sheina B Sim, Renée L Corpuz, Michael A Quail, Mara K N Lawniczak, Scott M Geib, Jonas Korlach, Megan Y Dennis

Abstract readPreprint
PubMed Full text at PMC Publisher
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

5 · Who and what money

Authors and funding

9 authors.

Sean P McGintyGenome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.
Gulhan KayaGenome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.
Sheina B SimU.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA.ORCID 0000-0003-0914-6914
Renée L CorpuzU.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA.
Michael A QuailWellcome Sanger Institute, Hinxton CB10 1SA, UK.
Mara K N LawniczakWellcome Sanger Institute, Hinxton CB10 1SA, UK.
Scott M GeibU.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA.
Jonas KorlachPacific Biosciences, Menlo Park, CA 94025, USA.
Megan Y DennisGenome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.ORCID 0000-0002-8502-5420

Funding

Human gene duplications in neurodevelopment and diseaseR01MH132818 · NIMH · UNIVERSITY OF CALIFORNIA AT DAVIS · PI DENNIS, MEGAN Y · 2023 to 2024
$1.4M
NIMH NIH HHS R01 MH132818Wellcome Trust
6 · The paper itself

Abstract

By coupling chromatin conformation capture (3C) with PacBio HiFi long-read sequencing, we have developed a new method (CiFi) that enables analysis of genome interactions across repetitive genomic regions with low-input requirements. CiFi produces multiple interacting concatemer segments per read, facilitating genome assembly and scaffolding. Together, the approach enables genomic analysis of previously recalcitrant low-complexity loci, and of small organisms such as single insect individuals.

Indexed as

Chromatin conformation captureCiFigenome assemblygenome organizationHiFilong-read sequencingPacBioscaffolding

Identifiers

PMID39975366
PMCPMC11838532

What Socratic 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 Socratic graph.