Evidence map›Paper›PMID 25748911›Full record

ArticleNature biotechnology2015

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek

Abstract readLetter
In one paragraph

Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 465 papers.

0numbers the graph read from it
0cells of the map it votes in
465citing 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

465 citing papers in PubMed.

  1. A Defined Strategy for Multi-Lineage Differentiation of Gastric Organoids.Methods in molecular biology (Clifton, N.J.) · 2027
    Article
  2. Article
  3. Integrative Transcriptomic Profiling Delineates LTBP4-Driven Fibroblast Reprogramming Across the Ossification Continuum of the Ligamentum Flavum.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026
    Article
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  12. Review
  13. Genes & diseases · 2026
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405 more citing papers are in PubMed but not listed here.

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.

Alyssa C Frazee1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.
Geo Pertea1] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Andrew E Jaffe1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [3] Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA.ORCID 0000000168861454
Ben Langmead1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [3] Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.
Steven L Salzberg1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [3] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [4] Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.ORCID 0000000288597432
Jeffrey T Leek1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.

Funding

Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7M
Statistical models for biological and technical variation in RNA sequencingR01GM105705 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI LEEK, JEFFREY T. · 2013 to 2017
$1.5M
NHGRI NIH HHS R01 HG006677NIGMS NIH HHS 1R01GM105705NIGMS NIH HHS R01 GM105705
6 · The paper itself

Abstract

PubMed holds no abstract for this paper.

Indexed as

Gene Expression RegulationSoftwareFemaleGene Expression ProfilingHumansMaleQuantitative Trait LociRNA, MessengerTranscriptomeRNA, Messenger

Identifiers

PMID25748911
PMCPMC4792117

What OpenQuestion holds

Textmetadata
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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.