Evidence map›Paper›PMID 36711469›Full record

ArticlebioRxiv : the preprint server for biology2023

Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model.

Ahsan Sanaullah, Degui Zhi, Shaojie Zhang

Open access · greenAbstract 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. 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, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors at 2 institutions in 1 country.

Ahsan SanaullahDepartment of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
Degui ZhiCenter for AI and Genome Informatics, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Shaojie ZhangDepartment of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
University of Central Florida · USThe University of Texas Health Science Center · US

Funding

Scalable methods for identity by descentR01HG010086 · NHGRI · YALE UNIVERSITY · PI Shaojie Zhang, Degui Zhi · 2018 to 2026
$4.9M
Genome Informatics For Biobank-scale DataR56HG011509 · NHGRI · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ZHANG, SHAOJIE, ZHI, DEGUI · 2021 to 2021
$616k
NHGRI NIH HHS R01 HG010086NHGRI NIH HHS R56 HG011509
6 · The paper itself

Abstract

The Li & Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel (haplotype threading). For small panels the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics, and has been the foundational model for haplotype phasing and imputation. However, LS becomes inefficient when sample size is large (tens of thousands to millions), because of its linear time complexity (

Identifiers

PMID36711469
PMCPMC9881975
OpenAlexW4313650079

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.