Joshua Paul

Josh is an engineer passionate about working at the intersection of biology, statistics, and computation. He was previously the Head of Bioinformatics at Invitae, where he built and supported a team responsible for delivering methods and software for the genomic analysis of millions of patients per year. He has led technical efforts ranging from the design and validation of novel statistical techniques to architecting enterprise software systems.

Josh received his PhD in Computer Science at UC Berkeley in Yun Song's group, where he worked on computationally tractable approaches to incorporating recombination in population genetic models. He received a BS in Physics and Computer Science at the University of Illinois.

Outside of work, Josh enjoys riding vintage bicycles, minimalist running, rock climbing, and cooking for his wife and two sons.


Truty, R., Paul, J.S., Kennemer, M., Lincoln, S.E., Olivares, E., Nussbaum, R.L., Aradhya, S. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genetics in Medicine, 21 (2019) 114-123.

Lincoln, S.E., Truty, R., Lin, C, Zook, J.M., Paul, J.S., Ramey, V.H., Salit, M., Rehm, H.L., Nussbaum, R.L.,Lebo, M.S. A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing. The Journal of Molecular Diagnostics, 21 (2019) 318-329.

Westbrook, M., Kvitek, D., Gafni, E., Paul, J.S., Kennemer, M., Winder, T., Shieh, P. Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Neurology, 90 (2018)

Steinr├╝cken, M., Paul, J.S., and Song, Y.S. A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theoretical Population Biology 87 (2013) 51-61.

Paul, J.S. and Song, Y.S. Blockwise HMM computation for large-scale population genomic inference. Bioinformatics, 28 (2012) 2008-2015.

Nielsen, R., Paul, J.S., Albrechtsen, A., and Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 12 (2011) 443-451.

Paul, J.S., Steinr├╝cken, M., and Song, Y.S. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187 (2011) 1115-1128

Paul, J.S. and Song, Y.S. A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics 186 (2010) 321-338.

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