Evidence map›Paper›PMID 39071335›Full record

ArticlebioRxiv : the preprint server for biology2025

Long-read sequencing transcriptome quantification with lr-kallisto.

Rebekah K Loving, Delaney K Sullivan, A Sina Booeshagi, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Y Liang, Ghassan Filimban, Shimako Kawauchi and 7 more

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

5 · Who and what money

Authors and funding

17 authors.

Rebekah K LovingDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0001-8725-0376
Delaney K SullivanDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0002-8359-6705
A Sina BooeshagiDepartment of Bioengineering, University of California, Berkeley, Berkeley, USA.ORCID 0000-0002-6442-4502
Fairlie ReeseDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-9240-0102
Elisabeth RebboahDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0003-2273-0189
Jasmine SakrDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-4470-3192
Narges RezaieDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0001-9326-9954
Heidi Y LiangDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-6190-9723
Ghassan FilimbanDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-2612-2554
Shimako KawauchiDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-8577-4763
Conrad OakesDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0002-8936-055X
Diane TroutDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0002-4928-5532
Brian A WilliamsDivision of Biology and Biological Engineering, California Institute of Technology, USA.
Grant MacGregorDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0001-7598-9501
Barbara J WoldDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0003-3235-8130
Ali MortazaviDevelopmental and Cell Biology, University of California Irvine, Irvine, USA.ORCID 0000-0002-4259-6362
Lior PachterDivision of Biology and Biological Engineering, California Institute of Technology, USA.ORCID 0000-0002-9164-6231

Funding

UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
Center for Mouse Genomic Variation at Single Cell ResolutionUM1HG012077 · NHGRI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Seyed Ali Mortazavi, BARBARA J WOLD · 2021 to 2026
$13.7M
Mentor Training to enhance mentorship in an interdisciplinary training programT32GM136624 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Arthur D Lander, Qing Nie · 2020 to 2026
$3.1M
NHGRI NIH HHS UM1 HG012077NIGMS NIH HHS T32 GM008042NIGMS NIH HHS T32 GM136624
6 · The paper itself

Abstract

RNA abundance quantification has become routine and affordable thanks to high-throughput "short-read" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. "Long-read" sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.

Identifiers

PMID39071335
PMCPMC11275803

What OpenQuestion holds

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Registered trials

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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.