Evidence map›Paper›PMID 36824968›Full record

ArticlebioRxiv : the preprint server for biology2023

Pairtools: from sequencing data to chromosome contacts.

Open2C, Nezar Abdennur, Geoffrey Fudenberg, Ilya M Flyamer, Aleksandra A Galitsyna, Anton Goloborodko, Maxim Imakaev, Sergey V Venev

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Open2C
Nezar AbdennurProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, MA.
Geoffrey FudenbergDepartment of Computational and Quantitative Biology, University of Southern California, Los Angeles, CA, USA.
Ilya M FlyamerFriedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
Aleksandra A GalitsynaInstitute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
Anton GoloborodkoInstitute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
Maxim ImakaevInstitute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
Sergey V VenevDepartment of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.

Funding

Center for 3D Structure and Physics of the GenomeUM1HG011536 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2020 to 2024
$11.8M
Genomes in 3D: from maps to mechanismsR35GM143116 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI FUDENBERG, GEOFFREY · 2021 to 2025
$2.1M
NHGRI NIH HHS UM1 HG011536NIGMS NIH HHS R35 GM143116
6 · The paper itself

Abstract

The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present

Identifiers

PMID36824968
PMCPMC9949071

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.