Smith JP - Search Results

1

Determinants of renin cell differentiation: a single cell epi-transcriptomics approach.

Martini AG, Smith JP, Medrano S, Sheffield NC, Sequeira-Lopez MLS, Gomez RA. Martini AG, et al. Among authors: smith jp. bioRxiv [Preprint]. 2023 Jan 20:2023.01.18.524595. doi: 10.1101/2023.01.18.524595. bioRxiv. 2023. PMID: 36711565 Free PMC article. Preprint.

2

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network; Greenleaf WJ, Chang HY. Corces MR, et al. Science. 2018 Oct 26;362(6413):eaav1898. doi: 10.1126/science.aav1898. Science. 2018. PMID: 30361341 Free PMC article.

3

Refgenie: a reference genome resource manager.

Stolarczyk M, Reuter VP, Smith JP, Magee NE, Sheffield NC. Stolarczyk M, et al. Among authors: smith jp. Gigascience. 2020 Feb 1;9(2):giz149. doi: 10.1093/gigascience/giz149. Gigascience. 2020. PMID: 31995185 Free PMC article.

4

Analytical Approaches for ATAC-seq Data Analysis.

Smith JP, Sheffield NC. Smith JP, et al. Curr Protoc Hum Genet. 2020 Jun;106(1):e101. doi: 10.1002/cphg.101. Curr Protoc Hum Genet. 2020. PMID: 32543102 Free PMC article.

5

COCOA: coordinate covariation analysis of epigenetic heterogeneity.

Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC. Lawson JT, et al. Among authors: smith jp. Genome Biol. 2020 Sep 7;21(1):240. doi: 10.1186/s13059-020-02139-4. Genome Biol. 2020. PMID: 32894181 Free PMC article.

6

PEPPRO: quality control and processing of nascent RNA profiling data.

Smith JP, Dutta AB, Sathyan KM, Guertin MJ, Sheffield NC. Smith JP, et al. Genome Biol. 2021 May 15;22(1):155. doi: 10.1186/s13059-021-02349-4. Genome Biol. 2021. PMID: 33992117 Free PMC article.

7

Embeddings of genomic region sets capture rich biological associations in lower dimensions.

Gharavi E, Gu A, Zheng G, Smith JP, Cho HJ, Zhang A, Brown DE, Sheffield NC. Gharavi E, et al. Among authors: smith jp. Bioinformatics. 2021 Dec 7;37(23):4299-4306. doi: 10.1093/bioinformatics/btab439. Bioinformatics. 2021. PMID: 34156475 Free PMC article.

8

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.

Smith JP, Corces MR, Xu J, Reuter VP, Chang HY, Sheffield NC. Smith JP, et al. NAR Genom Bioinform. 2021 Nov 23;3(4):lqab101. doi: 10.1093/nargab/lqab101. eCollection 2021 Dec. NAR Genom Bioinform. 2021. PMID: 34859208 Free PMC article.

9

GenomicDistributions: fast analysis of genomic intervals with Bioconductor.

Kupkova K, Mosquera JV, Smith JP, Stolarczyk M, Danehy TL, Lawson JT, Xue B, Stubbs JT 4th, LeRoy N, Sheffield NC. Kupkova K, et al. Among authors: smith jp. BMC Genomics. 2022 Apr 12;23(1):299. doi: 10.1186/s12864-022-08467-y. BMC Genomics. 2022. PMID: 35413804 Free PMC article.

10

Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development.

Duvall E, Benitez CM, Tellez K, Enge M, Pauerstein PT, Li L, Baek S, Quake SR, Smith JP, Sheffield NC, Kim SK, Arda HE. Duvall E, et al. Among authors: smith jp. Proc Natl Acad Sci U S A. 2022 Jun 28;119(26):e2201267119. doi: 10.1073/pnas.2201267119. Epub 2022 Jun 22. Proc Natl Acad Sci U S A. 2022. PMID: 35733248 Free PMC article.

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