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Jingmin Shu

dblp:432/2624 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2026
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
cancer genomics
1.012026
Competing subclones and fitness diversity shape tumor evolution across cancer types · Bioinform. 2026
Bioinformatics and computational biology › cancer genomics
tumor evolution
1.012026
Competing subclones and fitness diversity shape tumor evolution across cancer types · Bioinform. 2026
Bioinformatics and computational biology › cancer genomics › tumor heterogeneity
intra-tumor heterogeneity
0.312026
Competing subclones and fitness diversity shape tumor evolution across cancer types · Bioinform. 2026

Methods — techniques the papers use, named apart from their topics

population genetics modeling · 1.0bulk sequencing analysis · 1.0
YearPublicationVenuePosition
2026 Competing subclones and fitness diversity shape tumor evolution across cancer types
abstract
MOTIVATION: Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. RESULTS: We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. AVAILABILITY AND IMPLEMENTATION: R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).
Hai Chen, Jingmin Shu, Rekha Mudappathi, Elaine Li, Panwen Wang, Leif Bergsagel, Zhifu Sun, Logan Zhao, Changxin Shi, Jeffrey P. Townsend, Carlo Maley
Bioinform.2