Barr KA - Search Results

1

Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation.

Barr KA, Martinez C, Moran JR, Kim AR, Ramos AF, Reinitz J. Barr KA, et al. BMC Syst Biol. 2017 Nov 29;11(1):116. doi: 10.1186/s12918-017-0485-2. BMC Syst Biol. 2017. PMID: 29187214 Free PMC article.

2

A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design.

Martinez CA, Barr KA, Kim AR, Reinitz J. Martinez CA, et al. Among authors: barr ka. Methods. 2013 Jul 15;62(1):91-8. doi: 10.1016/j.ymeth.2013.05.014. Epub 2013 Jun 1. Methods. 2013. PMID: 23732772 Free PMC article.

3

A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.

Barr KA, Reinitz J. Barr KA, et al. PLoS One. 2017 Jul 17;12(7):e0180861. doi: 10.1371/journal.pone.0180861. eCollection 2017. PLoS One. 2017. PMID: 28715438 Free PMC article.

4

Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.

Barr KA, Reinitz J. Barr KA, et al. PLoS One. 2018 May 7;13(5):e0197211. doi: 10.1371/journal.pone.0197211. eCollection 2018. PLoS One. 2018. PMID: 29734377 Free PMC article.

5

An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.

Barr K, Reinitz J, Radulescu O. Barr K, et al. PLoS Comput Biol. 2019 Nov 15;15(11):e1007497. doi: 10.1371/journal.pcbi.1007497. eCollection 2019 Nov. PLoS Comput Biol. 2019. PMID: 31730659 Free PMC article.

6

Fully interpretable deep learning model of transcriptional control.

Liu Y, Barr K, Reinitz J. Liu Y, et al. Bioinformatics. 2020 Jul 1;36(Suppl_1):i499-i507. doi: 10.1093/bioinformatics/btaa506. Bioinformatics. 2020. PMID: 32657418 Free PMC article.

7

The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees.

Barr KA, Rhodes KL, Gilad Y. Barr KA, et al. Genome Biol. 2023 Sep 11;24(1):207. doi: 10.1186/s13059-023-03019-3. Genome Biol. 2023. PMID: 37697401 Free PMC article.

8

Egr2-dependent gene expression profiling and ChIP-Seq reveal novel biologic targets in T cell anergy.

Zheng Y, Zha Y, Spaapen RM, Mathew R, Barr K, Bendelac A, Gajewski TF. Zheng Y, et al. Mol Immunol. 2013 Oct;55(3-4):283-91. doi: 10.1016/j.molimm.2013.03.006. Epub 2013 Mar 30. Mol Immunol. 2013. PMID: 23548837 Free PMC article.

9

Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees.

Mittleman BE, Pott S, Warland S, Barr K, Cuevas C, Gilad Y. Mittleman BE, et al. Elife. 2021 Feb 17;10:e62548. doi: 10.7554/eLife.62548. Elife. 2021. PMID: 33595436 Free PMC article.

10

Elevated and sustained expression of the transcription factors Egr1 and Egr2 controls NKT lineage differentiation in response to TCR signaling.

Seiler MP, Mathew R, Liszewski MK, Spooner CJ, Barr K, Meng F, Singh H, Bendelac A. Seiler MP, et al. Nat Immunol. 2012 Feb 5;13(3):264-71. doi: 10.1038/ni.2230. Nat Immunol. 2012. PMID: 22306690 Free PMC article.

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