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Items: 1 to 20 of 29

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

Comprehensive genomic characterization of head and neck squamous cell carcinomas.

Cancer Genome Atlas Network.

Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129.

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.

Integrated genomic characterization of papillary thyroid carcinoma.

Cancer Genome Atlas Research Network.

Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050.

11.

Characterization of HPV and host genome interactions in primary head and neck cancers.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13.

12.

Comprehensive molecular profiling of lung adenocarcinoma.

Cancer Genome Atlas Research Network.

Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. Erratum in: Nature. 2014 Oct 9;514(7521):262. Rogers, K [corrected to Rodgers, K]. Nature. 2018 Jul;559(7715):E12.

13.

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.

14.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

15.

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.

16.

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.

17.

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.

18.

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.

19.

Comprehensive genomic characterization of squamous cell lung cancers.

Cancer Genome Atlas Research Network.

Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404. Epub 2012 Sep 9. Erratum in: Nature. 2012 Nov 8;491(7423):288. Rogers, Kristen [corrected to Rodgers, Kristen].

20.

Comprehensive molecular characterization of human colon and rectal cancer.

Cancer Genome Atlas Network.

Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252.

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