Evidence map›Paper›PMID 38386111›Full record

ArticleBulletin of mathematical biology2024

3D Genome Reconstruction from Partially Phased Hi-C Data.

Diego Cifuentes, Jan Draisma, Oskar Henriksson, Annachiara Korchmaros, Kaie Kubjas

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PubMed Full text at PMC Publisher
In one paragraph

Article in Bulletin of mathematical biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

5 authors.

Diego CifuentesSchool of Industrial and Systems Engineering, Georgia Institute of Technology, 755 Ferst Drive, NW, Atlanta, GA, 30332, USA.
Jan DraismaMathematisches Institut, University of Bern, Sidlerstrasse 5, 3012, Bern, Switzerland.
Oskar HenrikssonDepartment of Mathematical Sciences, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
Annachiara KorchmarosBioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
Kaie KubjasDepartment of Mathematics and Systems Analysis, Aalto University, P.O. Box 11100, 00076, Aalto, Finland. kaie.kubjas@aalto.fi.

Funding

Luonnontieteiden ja Tekniikan Tutkimuksen Toimikunta 323416Novo Nordisk NNF20OC0065582
6 · The paper itself

Abstract

The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruction method based on semidefinite programming, paired with numerical algebraic geometry and local optimization. The performance of this method is tested on several simulated datasets under different noise levels and with different amounts of phased data. We also apply it to a real dataset from mouse X chromosomes, and we are then able to recover previously known structural features.

Indexed as

Mathematical ConceptsModels, BiologicalAnimalsMice3D genome organizationApplied algebraic geometryDiploid organismsHi-CNumerical algebraic geometry

Identifiers

PMID38386111
PMCPMC10884149

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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.