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Items: 16

1.

An upstream enhancer regulates Gpihbp1 expression in a tissue-specific manner.

Allan CM, Heizer PJ, Tu Y, Sandoval NP, Jung RS, Morales JE, Sajti E, Troutman TD, Saunders TL, Cusanovich DA, Beigneux AP, Romanoski CE, Fong LG, Young SG.

J Lipid Res. 2019 Apr;60(4):869-879. doi: 10.1194/jlr.M091322. Epub 2018 Dec 31.

PMID:
30598475
2.

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J.

Science. 2018 Sep 28;361(6409):1380-1385. doi: 10.1126/science.aau0730. Epub 2018 Aug 30.

PMID:
30166440
3.

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C.

Mol Cell. 2018 Sep 6;71(5):858-871.e8. doi: 10.1016/j.molcel.2018.06.044. Epub 2018 Aug 2.

PMID:
30078726
4.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J.

Cell. 2018 Aug 23;174(5):1309-1324.e18. doi: 10.1016/j.cell.2018.06.052. Epub 2018 Aug 2.

PMID:
30078704
5.

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM.

Nature. 2018 Mar 22;555(7697):538-542. doi: 10.1038/nature25981. Epub 2018 Mar 14.

6.

Comprehensive single-cell transcriptional profiling of a multicellular organism.

Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J.

Science. 2017 Aug 18;357(6352):661-667. doi: 10.1126/science.aam8940.

7.

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J.

Am J Hum Genet. 2017 Aug 3;101(2):192-205. doi: 10.1016/j.ajhg.2017.06.010. Epub 2017 Jul 14.

8.

Mapping 3D genome architecture through in situ DNase Hi-C.

Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z.

Nat Protoc. 2016 Nov;11(11):2104-21. doi: 10.1038/nprot.2016.126. Epub 2016 Sep 29.

9.

Integrated analyses of gene expression and genetic association studies in a founder population.

Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, Decara JM, Gilad Y, Ober C.

Hum Mol Genet. 2016 May 15;25(10):2104-2112. Epub 2016 Feb 29.

10.

Genome-Wide Association Studies of the Human Gut Microbiota.

Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C, Gilad Y.

PLoS One. 2015 Nov 3;10(11):e0140301. doi: 10.1371/journal.pone.0140301. eCollection 2015.

11.

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J.

Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.

12.

The functional consequences of variation in transcription factor binding.

Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y.

PLoS Genet. 2014 Mar 6;10(3):e1004226. doi: 10.1371/journal.pgen.1004226. eCollection 2014 Mar.

13.

Primate transcript and protein expression levels evolve under compensatory selection pressures.

Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y.

Science. 2013 Nov 29;342(6162):1100-4. doi: 10.1126/science.1242379. Epub 2013 Oct 17.

14.

Regulatory element copy number differences shape primate expression profiles.

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.

15.

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.

Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y.

Hum Mol Genet. 2012 May 1;21(9):2111-23. doi: 10.1093/hmg/dds021. Epub 2012 Jan 27.

16.

The effects of EBV transformation on gene expression levels and methylation profiles.

Caliskan M, Cusanovich DA, Ober C, Gilad Y.

Hum Mol Genet. 2011 Apr 15;20(8):1643-52. doi: 10.1093/hmg/ddr041. Epub 2011 Feb 2. Erratum in: Hum Mol Genet. 2012 May 1;21(9):2142.

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