Author

J. Kelleher

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 5 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Assay:whole-genome sequencing· 4 Research Focus:benchmarking· 3 Approach:experimental assay· 3 Organism:human· 2 Research Focus:variant calling· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1

Frequent Co-Authors

G. McVean· 2 shared P. L. Ralph· 2 shared P. W. Messer· 2 shared S. Gravel· 2 shared Y. Wong· 2 shared A. D. Kern· 1 shared A. Durvasula· 1 shared A. Ignatieva· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersEvolutionary Biology

G. McVean

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Author profile →

6 papers

Recent·Most cited

A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2

S. H. Zhan, Y. Wong, A. Ignatieva, K. Eaton, I. Guthrie, B. Jeffery, D. S. Palmer, C. L. Murall, S. Otto, J. Kelleher

The paper infers an Ancestral Recombination Graph for 2.48 million SARS-CoV-2 genomes to account for recombination, providing a more accurate representation of viral genealogy than traditional trees.

bioRxiv · Jun 8, 2023 · PreprintEvolutionary Biology

Oncogenic metabolic rewiring independent of proliferative control in human mammary epithelial cells

W. Dong, M. A. Keibler, S. J. Moon, P. Cho, N. Liu, C. J. Berrios, J. Kelleher, H. D. Sikes, O. Iliopoulos, J. Coloff, M. Vander Heiden, G. Stephanopoulos

The paper compares metabolic flux in cancerous and normal human mammary epithelial cells using 13C-tracing and MFA, finding distinct metabolic pathways activated in cancer cells.

bioRxiv · Apr 8, 2022 · PreprintBiochemistry

A community-maintained standard library of population genetic models

J. R. Adrion, C. B. Cole, N. Dukler, J. G. Galloway, A. L. Gladstein, G. Gower, C. C. Kyriazis, A. P. Ragsdale, G. Tsambos, F. Baumdicker, J. Carlson, R. A. Cartwright, A. Durvasula, I. Gronau, B. Y. Kim, , A. D. Kern

The paper introduces stdpopsim, a community-maintained library for population genetic models, to standardize simulations and facilitate benchmarking of inference tools.

bioRxiv · Dec 20, 2019Evolutionary Biology

Coupling Wright-Fisher and coalescent dynamics for realistic simulation of population-scale datasets

D. Nelson, J. Kelleher, A. Ragsdale, G. McVean, S. Gravel

This paper extends the coalescent simulator msprime with a Wright-Fisher model to better simulate population-scale datasets, improving accuracy for long genomic regions and large samples.

bioRxiv · Jun 18, 2019Evolutionary Biology

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

B. C. Haller, J. Galloway, J. Kelleher, P. W. Messer, P. L. Ralph

The paper implements tree-sequence recording in SLiM 3 to improve computational efficiency and enable new analyses of whole-genome simulations.

bioRxiv · Nov 6, 2018Evolutionary Biology

Inferring the ancestry of everyone

J. Kelleher, Y. Wong, P. Albers, A. W. Wohns, G. McVean

The paper introduces an efficient algorithm for inferring whole-genome genealogies from large datasets, demonstrating its accuracy and scalability on human genetic data.

bioRxiv · Nov 1, 2018Evolutionary Biology