Kingsford C - Search Results

1

Detecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.

Ma C, Kingsford C. Ma C, et al. Among authors: kingsford c. Cell Syst. 2019 Dec 18;9(6):589-599.e7. doi: 10.1016/j.cels.2019.10.005. Epub 2019 Nov 27. Cell Syst. 2019. PMID: 31786209 Free PMC article.

2

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Patro R, Mount SM, Kingsford C. Patro R, et al. Among authors: kingsford c. Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20. Nat Biotechnol. 2014. PMID: 24752080 Free PMC article.

3

Salmon provides fast and bias-aware quantification of transcript expression.

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Patro R, et al. Among authors: kingsford c. Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. Nat Methods. 2017. PMID: 28263959 Free PMC article.

4

Accurate assembly of transcripts through phase-preserving graph decomposition.

Shao M, Kingsford C. Shao M, et al. Among authors: kingsford c. Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13. Nat Biotechnol. 2017. PMID: 29131147 Free PMC article.

5

SQUID: transcriptomic structural variation detection from RNA-seq.

Ma C, Shao M, Kingsford C. Ma C, et al. Among authors: kingsford c. Genome Biol. 2018 Apr 12;19(1):52. doi: 10.1186/s13059-018-1421-5. Genome Biol. 2018. PMID: 29650026 Free PMC article.

6

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.

Tung LH, Shao M, Kingsford C. Tung LH, et al. Among authors: kingsford c. Genome Biol. 2019 Dec 18;20(1):287. doi: 10.1186/s13059-019-1883-0. Genome Biol. 2019. PMID: 31849338 Free PMC article.

7

More Accurate Transcript Assembly via Parameter Advising.

Deblasio D, Kim K, Kingsford C. Deblasio D, et al. Among authors: kingsford c. J Comput Biol. 2020 Aug;27(8):1181-1189. doi: 10.1089/cmb.2019.0286. Epub 2020 Apr 21. J Comput Biol. 2020. PMID: 32315544 Free PMC article.

8

Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.

Qiu Y, Ma C, Xie H, Kingsford C. Qiu Y, et al. Among authors: kingsford c. Algorithms Mol Biol. 2020 May 15;15:9. doi: 10.1186/s13015-020-00170-5. eCollection 2020. Algorithms Mol Biol. 2020. PMID: 32467720 Free PMC article.

9

Alignment and mapping methodology influence transcript abundance estimation.

Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R. Srivastava A, et al. Among authors: kingsford c. Genome Biol. 2020 Sep 7;21(1):239. doi: 10.1186/s13059-020-02151-8. Genome Biol. 2020. PMID: 32894187 Free PMC article.

10

Exact transcript quantification over splice graphs.

Ma C, Zheng H, Kingsford C. Ma C, et al. Among authors: kingsford c. Algorithms Mol Biol. 2021 May 10;16(1):5. doi: 10.1186/s13015-021-00184-7. Algorithms Mol Biol. 2021. PMID: 33971903 Free PMC article.

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