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Items: 23

1.

Single-Cell Transcriptomic Analyses of Cell Fate Transitions during Human Cardiac Reprogramming.

Zhou Y, Liu Z, Welch JD, Gao X, Wang L, Garbutt T, Keepers B, Ma H, Prins JF, Shen W, Liu J, Qian L.

Cell Stem Cell. 2019 Jul 3;25(1):149-164.e9. doi: 10.1016/j.stem.2019.05.020. Epub 2019 Jun 20.

PMID:
31230860
2.

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte.

Liu Z, Wang L, Welch JD, Ma H, Zhou Y, Vaseghi HR, Yu S, Wall JB, Alimohamadi S, Zheng M, Yin C, Shen W, Prins JF, Liu J, Qian L.

Nature. 2017 Nov 2;551(7678):100-104. doi: 10.1038/nature24454. Epub 2017 Oct 25.

3.

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.

Welch JD, Hartemink AJ, Prins JF.

Genome Biol. 2017 Jul 24;18(1):138. doi: 10.1186/s13059-017-1269-0.

4.

Selective single cell isolation for genomics using microraft arrays.

Welch JD, Williams LA, DiSalvo M, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD.

Nucleic Acids Res. 2016 Sep 30;44(17):8292-301. doi: 10.1093/nar/gkw700. Epub 2016 Aug 16.

5.

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.

Welch JD, Hartemink AJ, Prins JF.

Genome Biol. 2016 May 23;17(1):106. doi: 10.1186/s13059-016-0975-3.

6.

Robust detection of alternative splicing in a population of single cells.

Welch JD, Hu Y, Prins JF.

Nucleic Acids Res. 2016 May 5;44(8):e73. doi: 10.1093/nar/gkv1525. Epub 2016 Jan 5.

7.

EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates.

Welch JD, Slevin MK, Tatomer DC, Duronio RJ, Prins JF, Marzluff WF.

RNA. 2015 Jul;21(7):1375-89. doi: 10.1261/rna.048785.114. Epub 2015 May 26.

8.

Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential.

Welch JD, Baran-Gale J, Perou CM, Sethupathy P, Prins JF.

BMC Genomics. 2015 Feb 22;16:113. doi: 10.1186/s12864-015-1227-8.

9.

Cache-Aware Asymptotically-Optimal Sampling-Based Motion Planning.

Ichnowski J, Prins JF, Alterovitz R.

IEEE Int Conf Robot Autom. 2014 May;2014:5804-5810.

10.

Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes.

Slevin MK, Meaux S, Welch JD, Bigler R, Miliani de Marval PL, Su W, Rhoads RE, Prins JF, Marzluff WF.

Mol Cell. 2014 Mar 20;53(6):1020-30. doi: 10.1016/j.molcel.2014.02.027.

11.

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects.

Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ.

Genome Res. 2014 Feb;24(2):241-50. doi: 10.1101/gr.158253.113. Epub 2013 Oct 24.

12.

BlackOPs: increasing confidence in variant detection through mappability filtering.

Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN.

Nucleic Acids Res. 2013 Oct;41(19):e178. doi: 10.1093/nar/gkt692. Epub 2013 Aug 8.

13.

A robust method for transcript quantification with RNA-seq data.

Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J.

J Comput Biol. 2013 Mar;20(3):167-87. doi: 10.1089/cmb.2012.0230.

14.

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.

15.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

16.

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.

Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27.

17.

A probabilistic framework for aligning paired-end RNA-seq data.

Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J.

Bioinformatics. 2010 Aug 15;26(16):1950-7. doi: 10.1093/bioinformatics/btq336. Epub 2010 Jun 23.

18.

A newly designed ergonomic body support for surgeons.

Albayrak A, van Veelen MA, Prins JF, Snijders CJ, de Ridder H, Kazemier G.

Surg Endosc. 2007 Oct;21(10):1835-40. Epub 2007 Mar 14.

PMID:
17356937
19.

Point-defect interactions when annealing diamonds implanted at low temperatures.

Prins JF.

Phys Rev B Condens Matter. 1991 Aug 1;44(6):2470-2479. No abstract available.

PMID:
9999816
20.

Fermi-Dirac statistics and the nature of the compensating donors in boron-doped diamond layers.

Prins JF.

Phys Rev B Condens Matter. 1989 Feb 15;39(6):3764-3770. No abstract available.

PMID:
9948698
21.

Activation of boron-dopant atoms in ion-implanted diamonds.

Prins JF.

Phys Rev B Condens Matter. 1988 Sep 15;38(8):5576-5584. No abstract available.

PMID:
9946999
22.

Volume expansion of diamond during ion implantation.

Prins JF, Derry TE, Sellschop JP.

Phys Rev B Condens Matter. 1986 Dec 15;34(12):8870-8874. No abstract available.

PMID:
9939610
23.

Onset of hopping conduction in carbon-ion-implanted diamond.

Prins JF.

Phys Rev B Condens Matter. 1985 Feb 15;31(4):2472-2478. No abstract available.

PMID:
9936062

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