Protocol for identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.

Mingyi Yang, Gege Liu, Magnar Bjørås, Junbai Wang

Abstract read

In one paragraph

Article in STAR protocols, 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

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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

4 authors.

Mingyi YangDepartment of Microbiology, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway. Electronic address: mingyiy@medisin.uio.no.

Gege LiuDepartment of Pathology, Oslo University Hospital - Norwegian Radium Hospital, 0372 Oslo, Norway.

Magnar BjøråsDepartment of Microbiology, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Centre for Embryology and Healthy Development, University of Oslo and Oslo University Hospital, 0316 Oslo, Norway.

Junbai WangDepartment of Clinical Molecular Biology (EpiGen), Akershus University Hospital and University of Oslo, 1478 Lørenskog, Norway; Faculty of Medicine, University of Oslo, 0316 Oslo, Norway. Electronic address: junbai.wang@medisin.uio.no.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Identifying functional mutation blocks (FMBs) that contribute to genome-wide transcriptional regulation remains a challenge. BayesPI-BAR version 3 (bpb3) is a Python-based tool for predicting FMBs by integrating DNA sequence data with gene expression data. Its application is demonstrated through four examples in two tasks: ranking transcription factors (TFs) most affected by 67 known single-nucleotide polymorphisms (SNPs) in regulatory regions and integrating the genomic distribution of SNPs with differential gene expression to identify FMBs that disrupt TF-DNA binding and gene expression in lymphoma. For complete details on the use and execution of this protocol, please refer to Yang et al.

Indexed as

BioinformaticsCancerComputer sciencesGeneticsGenomicsMolecular BiologySequence analysis

Identifiers

PMID42391005

DOI10.1016/j.xpro.2026.104642

PMCPMC13352380

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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.