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Items: 1 to 20 of 119

1.

RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq.

Svensson V, Pachter L.

Mol Cell. 2018 Oct 4;72(1):7-9. doi: 10.1016/j.molcel.2018.09.026.

PMID:
30290149
2.

Accurate design of translational output by a neural network model of ribosome distribution.

Tunney R, McGlincy NJ, Graham ME, Naddaf N, Pachter L, Lareau LF.

Nat Struct Mol Biol. 2018 Jul;25(7):577-582. doi: 10.1038/s41594-018-0080-2. Epub 2018 Jul 2.

PMID:
29967537
3.

Association mapping from sequencing reads using k-mers.

Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L.

Elife. 2018 Jun 13;7. pii: e32920. doi: 10.7554/eLife.32920.

4.

Gene-level differential analysis at transcript-level resolution.

Yi L, Pimentel H, Bray NL, Pachter L.

Genome Biol. 2018 Apr 12;19(1):53. doi: 10.1186/s13059-018-1419-z.

5.

Differential analysis of RNA-seq incorporating quantification uncertainty.

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L.

Nat Methods. 2017 Jul;14(7):687-690. doi: 10.1038/nmeth.4324. Epub 2017 Jun 5.

PMID:
28581496
6.

Pregnancy-induced gene expression changes in vivo among women with rheumatoid arthritis: a pilot study.

Goin DE, Smed MK, Pachter L, Purdom E, Nelson JL, Kjærgaard H, Olsen J, Hetland ML, Zoffmann V, Ottesen B, Jawaheer D.

Arthritis Res Ther. 2017 May 25;19(1):104. doi: 10.1186/s13075-017-1312-2.

7.

PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.

Li B, Tambe A, Aviran S, Pachter L.

Cell Syst. 2017 May 24;4(5):568-574.e7. doi: 10.1016/j.cels.2017.04.007. Epub 2017 May 10.

8.

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

Yi L, Pimentel H, Pachter L.

PLoS One. 2017 Apr 27;12(4):e0175744. doi: 10.1371/journal.pone.0175744. eCollection 2017.

9.

Pseudoalignment for metagenomic read assignment.

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L.

Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106.

10.

Hot topics, urgent priorities, and ensuring success for racial/ethnic minority young investigators in academic pediatrics.

Flores G, Mendoza FS, Fuentes-Afflick E, Mendoza JA, Pachter L, Espinoza J, Fernandez CR, Arnold DD, Brown NM, Gonzalez KM, Lopez C, Owen MC, Parks KM, Reynolds KL, Russell CJ.

Int J Equity Health. 2016 Dec 9;15(1):201.

11.

The Lair: a resource for exploratory analysis of published RNA-Seq data.

Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L.

BMC Bioinformatics. 2016 Dec 1;17(1):490.

12.

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements.

Fu AQ, Pachter L.

Stat Appl Genet Mol Biol. 2016 Dec 1;15(6):447-471. doi: 10.1515/sagmb-2016-0002.

13.

Single-cell analysis at the threshold.

Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA.

Nat Biotechnol. 2016 Nov 8;34(11):1111-1118. doi: 10.1038/nbt.3721. No abstract available.

PMID:
27824834
14.

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

Hateley S, Hosamani R, Bhardwaj SR, Pachter L, Bhattacharya S.

Genomics. 2016 Oct;108(3-4):158-167. doi: 10.1016/j.ygeno.2016.09.002. Epub 2016 Sep 10.

15.

Erratum: Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888d. No abstract available.

PMID:
27504780
16.

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts.

Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN.

Genome Biol. 2016 May 26;17(1):112. doi: 10.1186/s13059-016-0970-8.

17.

Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L.

Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4. Erratum in: Nat Biotechnol. 2016 Aug 9;34(8):888.

PMID:
27043002
18.

Pregnancy-Induced Changes in Systemic Gene Expression among Healthy Women and Women with Rheumatoid Arthritis.

Mittal A, Pachter L, Nelson JL, Kjærgaard H, Smed MK, Gildengorin VL, Zoffmann V, Hetland ML, Jewell NP, Olsen J, Jawaheer D.

PLoS One. 2015 Dec 18;10(12):e0145204. doi: 10.1371/journal.pone.0145204. eCollection 2015.

19.

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis.

Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB.

Science. 2015 Dec 4;350(6265):1251-5. doi: 10.1126/science.aad2456. Epub 2015 Nov 5.

20.

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG.

Nucleic Acids Res. 2016 Jan 29;44(2):838-51. doi: 10.1093/nar/gkv1168. Epub 2015 Nov 3.

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