Evidence map›Paper›PMID 38826299›Full record

ArticlebioRxiv : the preprint server for biology2024

MEM-based pangenome indexing for

Stephen Hwang, Nathaniel K Brown, Omar Y Ahmed, Katharine M Jenike, Sam Kovaka, Michael C Schatz, Ben Langmead

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

7 authors.

Stephen HwangXDBio Program, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0003-0299-569X
Nathaniel K BrownDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0002-6201-2301
Omar Y AhmedDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0002-9933-8508
Katharine M JenikeDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0002-7276-8110
Sam KovakaDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0002-4835-8023
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0002-4118-4446
Ben LangmeadDepartment of Computer Science, Johns Hopkins University, Baltimore MD, USA.ORCID 0000-0003-2437-1976

Funding

Methods for sequencing data analysis and archive-scale data science - RenewalR35GM139602 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Benjamin Thomas Langmead · 2021 to 2026
$5.0M
Personal and panel references for improved alignmentR01HG011392 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI LANGMEAD, BENJAMIN THOMAS · 2020 to 2025
$4.2M
Integrative genomic and epigenomic analysis of cancer using long read sequencingU01CA253481 · NCI · JOHNS HOPKINS UNIVERSITY · PI SCHATZ, MICHAEL · 2021 to 2023
$1.1M
NCI NIH HHS U01 CA253481NHGRI NIH HHS R01 HG011392NIGMS NIH HHS R35 GM139602
6 · The paper itself

Abstract

Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on

Indexed as

Applied computingComparative genomicsCompressed indexingComputational genomicsPangenomics

Identifiers

PMID38826299
PMCPMC11142109

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.