Evidence map›Paper›PMID 41279707›Full record

ArticlebioRxiv : the preprint server for biology2025

larch: mapping the parsimony-optimal landscape of trees for directed exploration.

Mary Barker, Ognian Milanov, Will Dumm, Dave Rich, Yatish Turakhia, Frederick A Matsen

Abstract readPreprint
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.

Mary BarkerComputational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0000-0002-7829-8017
Ognian MilanovHoward Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0009-0000-2885-1286
Will DummComputational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0000-0002-8617-476X
Dave RichComputational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0009-0005-2501-4032
Yatish TurakhiaDepartment of Electrical and Computer Engineering, University of California San Diego, San Diego, California, USA.ORCID 0000-0001-5600-2900
Frederick A MatsenComputational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.ORCID 0000-0003-0607-6025

Funding

Fast and flexible Bayesian phylogenetics via modern machine learningR01AI162611 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2021 to 2025
$3.8M
Blending deep learning with probabilistic mechanistic models to predict and understand the evolution and function of adaptive immune receptorsR01AI146028 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2019 to 2024
$3.4M
High-Performance Compute Cluster for Comprehensive Cancer and Infectious Diseases ResearchS10OD028685 · OD · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BRADLEY, PHILIP · 2020 to 2020
$2.0M
NIAID NIH HHS R01 AI146028NIAID NIH HHS R01 AI162611NIH HHS S10 OD028685
6 · The paper itself

Abstract

Phylogenetic inference algorithms for large data sets typically return a single tree. However, there are often many optimal trees, especially when sequence data is closely related. We develop a compact representation of large collections of maximally parsimonious

Identifiers

PMID41279707
PMCPMC12636427

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.