Bioinformatic methods, pipelines and resources developed by our lab
are freely available at our lab’s GitHub page.
spliTWAS
A new method to identify splicing TWAS
Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia
Hervoso JL, Amoah K, Dodson J, Choudhury M, Bhattacharya A, Quinones-Valdez G, Pasaniuc B, Xiao X.
isoLASER
A new method to examine haplotype-specific splicing in long-read RNA-seq data
Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
Quinones-Valdez G, Amoah K, Xiao X.
dsRID
A new method to identify long dsRNA regions using long-read RNA-seq data
dsRID: in silico identification of dsRNA regions using long-read RNA-seq data
Yamamoto R, Liu Z, Choudhury M, Xiao X.
scAllele
A new method for variant calling (SNPs and microindels) and allele-specific splicing analysis in single-cell RNA-seq data
scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Quinones-Valdez G, Fu T, Chan TW, Xiao X.
L-GIREMI
A new method to identify RNA editing sites using long-read RNA-seq
L-GIREMI uncovers RNA editing sites in long-read RNA-seq
Liu Z, Quinones-Valdez G, Fu T, Choudhury M, Reese F, Mortazavi A, Xiao X.
REDITs
A new method to identify differential RNA editing sites in RNA-sequencing data
Applicable to both small-scale replicated experimental designs and large-scale population cohorts
Tran SS, Zhou Q, Xiao X. Bioinformatics, 2020.
MountainClimber
A new method to identify alternative transcription start sites and polyadenylation sites in RNA-Seq
Cass AA, Xiao X. Cell Systems, 2019.
BEAPR
A new method to identify allele-specific binding of RNA-binding proteins in eCLIP-Seq data
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Yang EW, Bahn JH, Hsiao EYH, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X. Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w.
RBPs in RNA Editing
A resource that catalogs the impact of RNA-binding proteins on RNA editing, part of our ENCODE project.
Regulation of RNA editing by RNA-binding proteins in human cells
Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brummer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X.
Commun Biol. 2019 Jan 14;2:19. doi: 10.1038/s42003-018-0271-8. eCollection 2019.
RNA Editing in Autism Spectrum Disorders
A resource that catalogs RNA editomes in postmortem autistic brains
Widespread RNA editing dysregulation in brains from autistic individuals
Tran S, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YH, Lee C, Pratt GA, Martínez-Cerdeño V, Hagerman RJ, Yeo GW, Geschwind DH, Xiao X. Nat Neuroscience.
22(1), 25–36 (2019). Epub 2018 Dec 17.
GIREMI
A new method to identify RNA editing sites using RNA-Seq data without the need of genome sequencing
Genome sequence-independent identification of RNA editing sites.
Zhang Q, Xiao X. Nat Methods, 2015 Apr;12(4):347-50.
RASER
A new RNA-Seq read aligner that is good for applications of SNP finding and RNA editing identification
RASER: Reads Aligner for SNPs and Editing sites of RNA,
Anh J, Xiao X. Bioinformatics, 2015 Dec 15;31(24):3906-13.
ASARP
Software package for identification of Allele-Specific Alternative mRNA Processing (ASARP) in RNA-Seq data.
Identification of allele-specific alternative mRNA processing via transcriptome sequencing
Li G, Bahn JH, Lee JH, Peng G, Chen Z, Nelson SF, Xiao X. Nucleic Acids Research, 2012, 1–13, doi:10.1093/nar/gks280.