PFRED is a software tool for designing and analyzing antisense oligonucleotides and siRNA, offering customizable design criteria and open-source access.

PLoS ONE · Jan 22, 2021Peer-reviewedBioinformatics

ABACUS: A flexible UMI counter that leverages intronic reads for single-nucleus RNAseq analysis

Hualin Simon Xi, Lauren Gibilisco, Markus P. Kummer, Knut Biber, Astrid Wachter, Maya E. Woodbury

ABACUS improves sNuc-RNAseq analysis by incorporating intronic reads, doubling the number of identified nuclei in human brain data and enhancing cluster resolution.

bioRxiv · Nov 13, 2020 · PreprintBioinformatics

Profiling microglia from AD donors and non-demented elderly in acute human post-mortem cortical tissue

Astrid M. Alsema, Qiong Jiang, Laura Kracht, Emma Gerrits, Marissa Lisa Dubbelaar, Anneke Miedema, Nieske Brouwer, Elly M. Hol, Jinte Middeldorp, Roland E. van Dijk, Maya E. Woodbury, Astrid Wachter, Hualin Simon Xi, Thomas Möller, Knut Biber, , Bart J. L. Eggen

The paper profiles microglia transcriptomes in AD donors and non-demented elderly using bulk and single-cell RNA sequencing, finding no significant differences in gene expression or subcluster composition.

Frontiers in Molecular Neuroscience · Oct 28, 2020Peer-reviewedNeuroscience

Cell type specific genetic regulation of gene expression across human tissues

Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E. Castel, Andrew R. Hamel, Ana Viñuela, Amy L. Roberts, Serghei Mangul, Xiaoquan Wen, Gao T. Wang, Alvaro Barbeira, Diego Garrido-Martín, , Abhiram S. Rao

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

Science · Sep 10, 2020Peer-reviewedGenomics

Developmental And Genetic Regulation Of The Human Cortex Transcriptome In Schizophrenia

Andrew E. Jaffe, Richard E. Straub, Joo Heon Shin, Ran Tao, Yuan Gao, Leonardo Collado‐Torres, Tony Kam-Thong, Hualin Simon Xi, Jie Quan, Qiang Chen, Carlo Colantuoni, William S. Ulrich, Brady J. Maher, Amy Deep‐Soboslay, Alan J. Cross, , Daniel R. Weinberger

The paper identifies 237 genes associated with schizophrenia using RNA sequencing and eQTL analysis, showing enrichment for developmentally regulated synaptic genes.

Nature Neuroscience · Jul 19, 2018Peer-reviewedNeuroscience

A systematic survey of human tissue-specific gene expression and splicing reveals new opportunities for therapeutic target identification and evaluation

Robert Yang, Jie Quan, Reza Sodaei, François Aguet, Ayellet V. Segrè, John Allen, Thomas A. Lanz, Veronica Reinhart, Matthew E. Crawford, Samuel A. Hasson, Kristin Ardlie, Roderic Guigó, Hualin Simon Xi

The paper analyzes tissue-specific gene expression and splicing across 8527 RNA-seq samples to identify therapeutic targets and prioritize disease-associated genes.

bioRxiv · Apr 30, 2018 · PreprintGenomics