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Results: 1 to 20 of 126

1.

Rational experiment design for sequencing-based RNA structure mapping.

Aviran S, Pachter L.

RNA. 2014 Oct 20. [Epub ahead of print]

PMID:
25332375
[PubMed - as supplied by publisher]
2.

Adverse events in children: predictors of adult physical and mental conditions.

Van Niel C, Pachter LM, Wade R Jr, Felitti VJ, Stein MT.

J Dev Behav Pediatr. 2014 Oct;35(8):549-51. doi: 10.1097/DBP.0000000000000102.

PMID:
25225793
[PubMed - in process]
3.

Human intestinal tissue with adult stem cell properties derived from pluripotent stem cells.

Forster R, Chiba K, Schaeffer L, Regalado SG, Lai CS, Gao Q, Kiani S, Farin HF, Clevers H, Cost GJ, Chan A, Rebar EJ, Urnov FD, Gregory PD, Pachter L, Jaenisch R, Hockemeyer D.

Stem Cell Reports. 2014 Jun 3;2(6):838-52. doi: 10.1016/j.stemcr.2014.05.001. eCollection 2014 Jun 3. Erratum in: Stem Cell Reports. 2014 Jul 8;3(1):215.

PMID:
24936470
[PubMed - in process]
Free PMC Article
4.

Structural variation among wild and industrial strains of Penicillium chrysogenum.

Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB.

PLoS One. 2014 May 13;9(5):e96784. doi: 10.1371/journal.pone.0096784. eCollection 2014.

PMID:
24824901
[PubMed - in process]
Free PMC Article
5.

Efforts to diversify the academic pediatric workforce.

Thompson DA, Pachter LM, Keller D.

JAMA Pediatr. 2014 Apr;168(4):390-1. doi: 10.1001/jamapediatrics.2013.4867. No abstract available.

PMID:
24710589
[PubMed - indexed for MEDLINE]
6.

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity.

Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D.

Genome Res. 2014 May;24(5):821-30. doi: 10.1101/gr.162412.113. Epub 2014 Feb 20.

PMID:
24558263
[PubMed - in process]
Free Article
7.

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2014 Apr;42(6):4031-42. doi: 10.1093/nar/gkt1388. Epub 2014 Jan 17.

PMID:
24442673
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Fragment assignment in the cloud with eXpress-D.

Roberts A, Feng H, Pachter L.

BMC Bioinformatics. 2013 Dec 7;14:358. doi: 10.1186/1471-2105-14-358.

PMID:
24314033
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB.

Curr Protoc Chem Biol. 2012 Dec 1;4(4):275-97. doi: 10.1002/9780470559277.ch120019.

PMID:
23788555
[PubMed]
10.

Updating RNA-Seq analyses after re-annotation.

Roberts A, Schaeffer L, Pachter L.

Bioinformatics. 2013 Jul 1;29(13):1631-7. doi: 10.1093/bioinformatics/btt197. Epub 2013 May 14.

PMID:
23677943
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

CGAL: computing genome assembly likelihoods.

Rahman A, Pachter L.

Genome Biol. 2013 Jan 29;14(1):R8. doi: 10.1186/gb-2013-14-1-r8.

PMID:
23360652
[PubMed - in process]
Free PMC Article
12.

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L.

Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9.

PMID:
23222703
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Streaming fragment assignment for real-time analysis of sequencing experiments.

Roberts A, Pachter L.

Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18.

PMID:
23160280
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Quantifying uniformity of mapped reads.

Hower V, Starfield R, Roberts A, Pachter L.

Bioinformatics. 2012 Oct 15;28(20):2680-2. doi: 10.1093/bioinformatics/bts451. Epub 2012 Jul 18.

PMID:
22815359
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Complementary and alternative medicine use and adherence with pediatric asthma treatment.

Philp JC, Maselli J, Pachter LM, Cabana MD.

Pediatrics. 2012 May;129(5):e1148-54. doi: 10.1542/peds.2011-2467. Epub 2012 Apr 9.

PMID:
22492763
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A closer look at RNA editing.

Pachter L.

Nat Biotechnol. 2012 Mar 7;30(3):246-7. doi: 10.1038/nbt.2156. No abstract available.

PMID:
22398619
[PubMed - indexed for MEDLINE]
17.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.

PMID:
22383036
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

RNA-Seq and find: entering the RNA deep field.

Roberts A, Pachter L.

Genome Med. 2011 Nov 22;3(11):74. doi: 10.1186/gm290.

PMID:
22113004
[PubMed]
Free PMC Article
19.

Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.

PMID:
22099972
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states.

Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D.

Genome Res. 2011 Dec;21(12):2049-57. doi: 10.1101/gr.122721.111. Epub 2011 Sep 9.

PMID:
21908772
[PubMed - indexed for MEDLINE]
Free PMC Article

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