Computer Science Research Works

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Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
(Springer Nature, 2011-09-28) Niranjan, Tejasvi S; Adamczyk, Abby; Bravo, Héctor Corrada; Taub, Margaret A; Wheelan, Sarah J; Irizarry, Rafael; Wang, Tao
Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Srfim) and filtering (SERVIC4E) algorithms. We sequenced 24 exons in two cohorts of 480 samples each, identifying 47 coding variants, including 30 present once per cohort. Validation by Sanger sequencing revealed an excellent combination of sensitivity and specificity for variant detection in pooled samples of both cohorts as compared to publicly available algorithms.
Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
(Springer Nature, 2019-08-13) Gunady, Mohamed K; Mount, Stephen M; Bravo, Héctor Corrada
Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step.