Improved analysis methods for RNA-seq

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Carl Kingsford
Herbert A. Simon Professor of Computer Science

Publications

(2021). Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism. bioRxiv, doi: https://doi.org/10.1101/2021.01.17.426996.

Preprint Project

(2020). Exact Transcript Quantification Over Splice Graphs. In Proceedings of WABI 2020; journal version in Alg. Mol. Bio. 2021.

PDF Project DOI Journal Version

(2019). Finding ranges of optimal transcript expression quantification in cases of non-identifiability. RECOMB 2021.

Preprint Code Project DOI

(2019). Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification. Cell Systems 9:1-11.

Preprint PDF Code Project Project DOI pubmed

(2019). Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 18:1–18:19 (2019); journal version in Alg Mol Bio (2020).

Preprint PDF Project Project DOI Journal Version

(2019). Alignment and mapping methodology influence transcript abundance estimation. bioRxiv.

Preprint Dataset Project DOI

(2019). Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads. Genome Biology 20:287.

Preprint PDF Project DOI

(2019). More accurate transcript assembly via parameter advising. The 2019 ICML Workshop on Computational Biology; journal version in Journal of Computational Biology.

Preprint PDF Code Project Project

(2018). SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biology 19:52.

Preprint PDF Code Project Project

(2017). Accurate assembly of transcripts through phase-preserving graph decomposition. Nature Biotechnology 35:1167-1169.

Preprint PDF Code Project

(2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14:417-419.

Preprint PDF Code Project Project

(2014). Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology 32:462-464.

PDF Code Project Project