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On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library.
Bioinformatics. 2022 Mar 4;38(6):1491-1496. doi: 10.1093/bioinformatics/btab873.
Bioinformatics. 2022.
PMID: 34978563
Free PMC article.
COSINE: non-seeding method for mapping long noisy sequences.
Afshar PT, Wong WH.
Afshar PT, et al.
Nucleic Acids Res. 2017 Aug 21;45(14):e132. doi: 10.1093/nar/gkx511.
Nucleic Acids Res. 2017.
PMID: 28586438
Free PMC article.
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Characterization of the human ESC transcriptome by hybrid sequencing.
Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH.
Au KF, et al. Among authors: afshar pt.
Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4821-30. doi: 10.1073/pnas.1320101110. Epub 2013 Nov 26.
Proc Natl Acad Sci U S A. 2013.
PMID: 24282307
Free PMC article.
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Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.
Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK.
Sahraeian SME, et al. Among authors: afshar pt.
Nat Commun. 2017 Jul 5;8(1):59. doi: 10.1038/s41467-017-00050-4.
Nat Commun. 2017.
PMID: 28680106
Free PMC article.
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Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF.
Weirather JL, et al. Among authors: afshar pt.
Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3.
Nucleic Acids Res. 2015.
PMID: 26040699
Free PMC article.
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An ensemble approach to accurately detect somatic mutations using SomaticSeq.
Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY.
Fang LT, et al. Among authors: afshar pt.
Genome Biol. 2015 Sep 17;16(1):197. doi: 10.1186/s13059-015-0758-2.
Genome Biol. 2015.
PMID: 26381235
Free PMC article.
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A universal SNP and small-indel variant caller using deep neural networks.
Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA.
Poplin R, et al. Among authors: afshar pt.
Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24.
Nat Biotechnol. 2018.
PMID: 30247488
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