Thomson JA - Search Results

1

Evaluation of de novo transcriptome assemblies from RNA-Seq data.

Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Li B, et al. Among authors: thomson ja. Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5. Genome Biol. 2014. PMID: 25608678 Free PMC article.

2

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.

Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM. Kim YJ, et al. Among authors: thomson ja. Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7. Bioinformatics. 2009. PMID: 19351619 Free PMC article.

3

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. Li B, et al. Among authors: thomson ja. Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18. Bioinformatics. 2010. PMID: 20022975 Free PMC article.

4

Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells.

Hu K, Yu J, Suknuntha K, Tian S, Montgomery K, Choi KD, Stewart R, Thomson JA, Slukvin II. Hu K, et al. Among authors: thomson ja. Blood. 2011 Apr 7;117(14):e109-19. doi: 10.1182/blood-2010-07-298331. Epub 2011 Feb 4. Blood. 2011. PMID: 21296996 Free PMC article.

5

TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM).

Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H. Nie J, et al. Among authors: thomson ja. BMC Syst Biol. 2011 Apr 15;5:53. doi: 10.1186/1752-0509-5-53. BMC Syst Biol. 2011. PMID: 21496241 Free PMC article.

6

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R. Sengupta S, et al. Among authors: thomson ja. J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340. J Vis Exp. 2011. PMID: 22064688 Free PMC article.

7

Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells.

Feng X, Zhang J, Smuga-Otto K, Tian S, Yu J, Stewart R, Thomson JA. Feng X, et al. Among authors: thomson ja. Stem Cells. 2012 Mar;30(3):461-70. doi: 10.1002/stem.1018. Stem Cells. 2012. PMID: 22213079 Free PMC article.

8

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C. Leng N, et al. Among authors: thomson ja. Bioinformatics. 2013 Apr 15;29(8):1035-43. doi: 10.1093/bioinformatics/btt087. Epub 2013 Feb 21. Bioinformatics. 2013. PMID: 23428641 Free PMC article.

9

Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.

Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN. Stewart R, et al. Among authors: thomson ja. PLoS Comput Biol. 2013;9(3):e1002936. doi: 10.1371/journal.pcbi.1002936. Epub 2013 Mar 7. PLoS Comput Biol. 2013. PMID: 23505351 Free PMC article.

10

Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents.

Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA. Meyer S, et al. Among authors: thomson ja. PLoS One. 2013 Aug 13;8(8):e71798. doi: 10.1371/journal.pone.0071798. eCollection 2013. PLoS One. 2013. PMID: 23967247 Free PMC article.

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