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Publications

Analysis-ready VCF at Biobank scale using Zarr.

Czech E. et al, (2024), bioRxiv

tstrait: a quantitative trait simulator for ancestral recombination graphs.

Tagami D. et al, (2024), Bioinformatics (Oxford, England)

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.

Lauterbur ME. et al, (2023), eLife, 12

Efficient ancestry and mutation simulation with msprime 1.0.

Baumdicker F. et al, (2021), Genetics

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Rehm HL. et al, (2021), Cell genomics, 1

Lessons Learned from Bugs in Models of Human History.

Ragsdale AP. et al, (2020), American journal of human genetics, 107, 583 - 588

Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes

Ralph P. et al, (2020), Genetics, 215, 779 - 797

A community-maintained standard library of population genetic models

Adrion JR. et al, (2020), eLife, 9

Accounting for long-range correlations in genome-wide simulations of large cohorts

Nelson D. et al, (2020), PLOS Genetics, 16, e1008619 - e1008619

Publisher Correction: Inferring whole-genome histories in large population datasets

Kelleher J. et al, (2019), Nature Genetics, 51, 1660 - 1660

Inferring whole-genome histories in large population datasets

Kelleher J. et al, (2019), Nature Genetics, 51, 1330 - 1338

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

Nelson D. et al, (2019)

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

Haller BC. et al, (2019), Molecular ecology resources, 19, 552 - 566

htsget: a protocol for securely streaming genomic data

Kelleher J. et al, (2019), Bioinformatics, 35, 119 - 121

Efficient pedigree recording for fast population genetics simulation

Kelleher J. et al, (2018), PLOS Computational Biology, 14, e1006581 - e1006581

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning B. et al, (2018), Nature Methods, 15, 475 - 476

Efficient pedigree recording for fast population genetics simulation

Kelleher J. et al, (2018)

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

Kelleher J. et al, (2016), PLOS Computational Biology, 12, e1004842 - e1004842

Spread of pedigree versus genetic ancestry in spatially distributed populations

Kelleher J. et al, (2016), Theoretical Population Biology, 108, 1 - 12

Efficient coalescent simulation and genealogical analysis for large sample sizes

Kelleher J. et al, (2015)

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