Doctor of Philosophy, University of California Berkeley (2016)
Master of Arts, University of California Berkeley (2013)
Bachelor of Science, California State University, Fullerton (2010)
High school diploma, La Mirada High School (2005)
Jonathan Pritchard, Postdoctoral Faculty Sponsor
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
2017; 12 (4)
A recent study of the gene expression patterns of Zika virus (ZIKV) infected human neural progenitor cells (hNPCs) revealed transcriptional dysregulation and identified cell cycle-related pathways that are affected by infection. However deeper exploration of the information present in the RNA-Seq data can be used to further elucidate the manner in which Zika infection of hNPCs affects the transcriptome, refining pathway predictions and revealing isoform-specific dynamics.We analyzed data published by Tang et al. using state-of-the-art tools for transcriptome analysis. By accounting for the experimental design and estimation of technical and inferential variance we were able to pinpoint Zika infection affected pathways that highlight Zika's neural tropism. The examination of differential genes reveals cases of isoform divergence.Transcriptome analysis of Zika infected hNPCs has the potential to identify the molecular signatures of Zika infected neural cells. These signatures may be useful for diagnostics and for the resolution of infection pathways that can be used to harvest specific targets for further study.
View details for DOI 10.1371/journal.pone.0175744
View details for Web of Science ID 000400383600023
View details for PubMedID 28448519
Pseudoalignment for metagenomic read assignment.
Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains.We find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics projects.Pipeline and analysis code can be downloaded from http://github.com/pachterlab/metakallisto .email@example.com.
View details for DOI 10.1093/bioinformatics/btx106
View details for PubMedID 28334086