Publications
- Alquicira-Hernandez J., Powell J. E., Phan T. G.. No evidence
that plasmablasts transdifferentiate into developing neutrophils in
severe COVID-19 disease. Clinical & Translational Immunology 10
(7), e1308. (2020).
https://doi.org/10.1002/cti2.1308 - Võsa U., Claringbould A., Westra H-J., Bonder M. J., Deelen P, ...,
Alquicira-Hernandez J., et al, Powell J. E., Gibson G., Esko T.,
Franke L.. Large-scale cis- and trans-eQTL analyses identify
thousands of genetic loci and polygenic scores that regulate blood
gene expression. (2020). Nature Genetics in Press.
https://doi.org/10.1101/447367 - Alquicira-Hernandez J., Powell J. E. Nebulosa recovers
single-cell gene expression signals by kernel density estimation.
Bioinformatics, btab003. (2021).
https://doi.org/10.1093/bioinformatics/btab003 - Avila Cobos, F., Alquicira-Hernandez, J., Powell, J.E. Mestdagh
P., De Preter K.. Benchmarking of cell type deconvolution
pipelines for transcriptomics data. Nature Communications
11, 5650. (2020).
https://doi.org/10.1038/s41467-020-19015-1 - Chavez J., Barberena-Jonas C., Sotelo-Fonseca J. E.,
Alquicira-Hernandez J., Salgado H, Collado-Torres L., Reyes A.
Programmatic access to bacterial regulatory networks with
regutools, Bioinformatics, 36, 16, 15, 4532–4534 (2020),
https://doi.org/10.1093/bioinformatics/btaa575 - Alquicira-Hernandez J., Sathe A., P Ji H., Nguyen Q., Powell J.
E. scPred: accurate supervised method for cell-type
classification from single-cell RNA-seq data.. Genome Biology.
(2019).
https://doi.org/10.1101/369538 - Senabouth A., Lukowski S., Alquicira-Hernandez J., Andersen S.,
Mei X., Nguyen Q., Powell J. E. (2019). ascend: R package for
analysis of single cell RNA-seq data. GigaScience.
https://doi.org/10.1093/gigascience/giz087 - Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernandez J ,
Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD,
Langmead B, Leek JT (2016). Human splicing diversity across the
Sequence Read Archive. Genome Biology.
https://doi.org/10.1186/s13059-016-1118-6 - Nellore A., Collado-Torres L., Jaffe A. E.,
Alquicira-Hernandez J. , Pritt J., Morton J., Leek J. T.,
Langmead B. (2016). Rail-RNA: Scalable analysis of RNA-seq
splicing and coverage. Bioinformatics
https://doi:10.1093/bioinformatics/btw575