Evidence map›Paper›PMID 41040245›Full record

ArticlebioRxiv : the preprint server for biology2025

Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes.

Ales Varabyou, Mykhaylo Artamonov, Sophia Cheng, Diane L Bolton, Steven L Salzberg, Mihaela Pertea

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

6 authors.

Ales VarabyouDepartment of Biomedical Engineering, Johns Hopkins University; Baltimore, MD.ORCID 0000-0003-1060-7212
Mykhaylo ArtamonovUS Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD.
Sophia ChengUS Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD.
Diane L BoltonUS Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD.
Steven L SalzbergDepartment of Biomedical Engineering, Johns Hopkins University; Baltimore, MD.ORCID 0000-0002-8859-7432
Mihaela PerteaDepartment of Biomedical Engineering, Johns Hopkins University; Baltimore, MD.

Funding

Exploring new approaches for enhanced human gene annotationR35GM156470 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Mihaela Pertea · 2025 to 2026
$776k
NIGMS NIH HHS R35 GM156470
6 · The paper itself

Abstract

Alternative splicing in HIV-1 has been a central focus of decades of research, uncovering key mechanisms of viral gene regulation, immune evasion, and therapeutic response - yet, no reference resource has existed to support transcriptome-wide analysis, limiting adoption of modern computational methods. We present HIV Atlas (https://ccb.jhu.edu/HIV_Atlas), the first reference-quality annotation of HIV-1 and SIV transcriptional diversity. We manually curated transcriptomes for HIV-1

Identifiers

PMID41040245
PMCPMC12485963

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.