Evidence map›Paper›PMID 42613741›Full record

ArticleBioinformatics (Oxford, England)2026

PangyPlot: multi-scale interactive visualization of pangenome variation graphs.

Scott Mastromatteo, Shalvi Chirmade, Delnaz Roshandel, Bhooma Thiruvahindrapuram, Zhuozhi Wang, Rohan V Patel, Wilson W L Sung, Amirhossein Hajianpour, Cheng Wang, Fan Lin and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2026. 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

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

16 authors.

Scott MastromatteoProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0002-3551-2247
Shalvi ChirmadeProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0009-0002-2015-6718
Delnaz RoshandelProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0002-4902-8587
Bhooma ThiruvahindrapuramThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0003-1128-008X
Zhuozhi WangThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0002-5169-5266
Rohan V PatelThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0001-8674-9706
Wilson W L SungDepartment of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, M5G 1H3, Canada.ORCID 0000-0002-4703-5118
Amirhossein HajianpourThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0009-0004-3741-8694
Cheng WangProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
Fan LinProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
Katherine KeenanProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0003-4656-4488
Julie AvolioTranslational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0003-0270-3941
Paul D W EckfordMission Programs, Cystic Fibrosis Canada, Toronto, ON, M4R 1K8, Canada.
Felix RatjenTranslational Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0003-4057-6592
Canadian Cystic Fibrosis Gene Modifier Consortium
Lisa J StrugProgram in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.ORCID 0000-0003-0503-9740

Funding

CF Canada 2022 Basic and Clinical Research Grant 1009794CIHR FRN-167282Cystic Fibrosis Canada 608828Cystic Fibrosis Canada and the CIHR Institute of Circulatory and Respiratory Health 187014Cystic Fibrosis Foundation (STRUG17PO)Government of Canada through Genome Canada and the Ontario Genomics Institute OGI-148The Centre for Applied Genomics
6 · The paper itself

Abstract

summaryPangenome variation graphs integrate multiple samples into a unified representation, mitigating the reference bias inherent to linear genomes. However, these graphs can be large and structurally complex. Existing visualization tools are each confined to a fixed scale of resolution, requiring researchers to switch between multiple tools to examine variation at different levels of detail. PangyPlot is an interactive pangenome browser designed for multi-scale exploration of reference variation graphs from full chromosome to nucleotide-level sequence segments. PangyPlot anchors navigation to linear reference coordinates, organizes variation into hierarchical bubble structures, and uses a force-directed layout engine for automatic node arrangement. AVAILABILITY AND IMPLEMENTATION: An instance preloaded with data is available at https://pangyplot.research.sickkids.ca. Source code and documentation are openly available at https://github.com/strug-hub/pangyplot under the MIT License.

Indexed as

Computer GraphicsGenetic VariationGenomeGenomicsSoftware

Identifiers

PMID42613741
PMCPMC13523859

What OpenQuestion holds

Textmetadata
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.