Publications

Learn more about the work we do in the Yang Lab through our selected publications. For a full list, please visit Google Scholar or Pubmed.

ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations
Schäfer et al. Bioinformatcis (2023)

PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
Li & Yang. bioRxiv (2023)

Expression and Therapeutic Targeting of TROP-2 in Treatment-Resistant Prostate Cancer
Sperger et al. Clinical Cancer Research (2023)

ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data
Fry et al. Bioinformatics (2022)

Detecting Medium and Large Insertions and Deletions with transIndel
Wang and Yang. Variant Calling: Methods and Protocols (2022)

Histone Deacetylase Sirtuin 1 Promotes Loss of Primary Cilia in Cholangiocarcinoma
Pant et al. Hepatology (2021)

LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data
Ren et al. BMC Genomics (2021)

Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer
Che et al. Nature Communications (2021)

Identification of mutations that cooperate with defects in B cell transcription factors to initiate leukemia
Heltemes-Harris et al. Oncogene (2021)

Integrated protocol for exitron and exitron-derived neoantigen identification using human RNA-seq data with ScanExitron and ScanNeo
Wang and Yang. STAR Protocols (2021)

A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes
Wang et al. Molecular Cell (2021)

ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation
Wang et al. GigaScience (2020)

The DNA methylation landscape of advanced prostate cancer
Zhao et al. Nature Genetics (2020)

Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer
Li et al. Clinical Cancer Research (2020)

ScanNeo: identifying indel-derived neoantigens using RNA-Seq data
Wang et al. Bioinformatics (2019)

Indel detection from DNA and RNA sequencing data with transIndel
Yang et al. BMC Genomics (2018)

Targeting a single alternative polyadenylation site coordinately blocks expression of androgen receptor mRNA splice variants in prostate cancer
Van Etten et al. Cancer Research (2017)

Androgen receptor variant AR-V9 is coexpressed with AR-V7 in prostate cancer metastases and predicts abiraterone resistance
Kohli et al. Clinical Cancer Research (2017)

Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival
Katerndahl et al. Nature Immunology (2017)

Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer
Henzler et al. Nature Communications (2016)

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
Yang et al. Genome Medicine (2015)

Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer
Asangani et al. Nature (2014)