Improved analysis methods for RNA-seq
Publications
Avi Srivastava,
Mohsen Zakeri,
Hirak Sarkar,
Charlotte Soneson,
Carl Kingsford,
Rob Patro
(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.
Cong Ma,
Hongyu Zheng,
Carl Kingsford
(2020).
Exact Transcript Quantification Over Splice Graphs.
In Proceedings of WABI 2020; journal version in Alg. Mol. Bio. 2021.
Cong Ma,
Hongyu Zheng,
Carl Kingsford
(2019).
Finding ranges of optimal transcript expression quantification in cases of non-identifiability.
RECOMB 2021.
Cong Ma,
Carl Kingsford
(2019).
Detecting, categorizing, and correcting coverage anomalies of RNA-seq quantification.
Cell Systems 9:1-11.
Yutong Qiu,
Cong Ma,
Han Xie,
Carl Kingsford
(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).
Avi Srivastava,
Laraib Malik,
Mohsen Zakeri,
Hirak Sarkar,
Charlotte Soneson,
Michael I Love,
Carl Kingsford,
Rob Patro
(2019).
Alignment and mapping methodology influence transcript abundance estimation.
bioRxiv.
Laura H. Tung,
Mingfu Shao,
Carl Kingsford
(2019).
Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads.
Genome Biology 20:287.
Dan DeBlasio,
Kwanho Kim,
Carl Kingsford
(2019).
More accurate transcript assembly via parameter advising.
The 2019 ICML Workshop on Computational Biology; journal version
in Journal of Computational Biology.
Cong Ma,
Mingfu Shao,
Carl Kingsford
(2018).
SQUID: transcriptomic structural variation detection from RNA-seq.
Genome Biology 19:52.
Mingfu Shao,
Carl Kingsford
(2017).
Accurate assembly of transcripts through phase-preserving graph decomposition.
Nature Biotechnology 35:1167-1169.
Rob Patro,
Geet Duggal,
Michael I Love,
Rafael A Irizarry,
Carl Kingsford
(2017).
Salmon provides fast and bias-aware quantification of transcript expression.
Nature Methods 14:417-419.
Rob Patro,
Stephen M Mount,
Carl Kingsford
(2014).
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
Nature Biotechnology 32:462-464.