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Items: 1 to 20 of 55

1.

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets.

Lareau C, Kangeyan D, Aryee MJ.

Methods Mol Biol. 2019;1935:187-202. doi: 10.1007/978-1-4939-9057-3_13.

PMID:
30758828
2.

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK.

Nat Biotechnol. 2019 Feb 11. doi: 10.1038/s41587-018-0011-0. [Epub ahead of print]

PMID:
30742127
3.

Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq.

Lazzarotto CR, Nguyen NT, Tang X, Malagon-Lopez J, Guo JA, Aryee MJ, Joung JK, Tsai SQ.

Nat Protoc. 2018 Nov;13(11):2615-2642. doi: 10.1038/s41596-018-0055-0.

PMID:
30341435
4.

In vivo CRISPR editing with no detectable genome-wide off-target mutations.

Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK.

Nature. 2018 Sep;561(7723):416-419. doi: 10.1038/s41586-018-0500-9. Epub 2018 Sep 12.

PMID:
30209390
5.

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

Pelikan RC, Kelly JA, Fu Y, Lareau CA, Tessneer KL, Wiley GB, Wiley MM, Glenn SB, Harley JB, Guthridge JM, James JA, Aryee MJ, Montgomery C, Gaffney PM.

Nat Commun. 2018 Jul 25;9(1):2905. doi: 10.1038/s41467-018-05328-9.

6.

Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize.

Lee K, Zhang Y, Kleinstiver BP, Guo JA, Aryee MJ, Miller J, Malzahn A, Zarecor S, Lawrence-Dill CJ, Joung JK, Qi Y, Wang K.

Plant Biotechnol J. 2019 Feb;17(2):362-372. doi: 10.1111/pbi.12982. Epub 2018 Jul 22.

7.

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ.

Cell. 2018 May 31;173(6):1535-1548.e16. doi: 10.1016/j.cell.2018.03.074. Epub 2018 Apr 26.

PMID:
29706549
8.

Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo".

Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L.

Nat Methods. 2018 Apr;15(4):238-239. doi: 10.1038/nmeth.4541. Epub 2018 Mar 30. No abstract available.

PMID:
29600992
9.

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data.

Lareau CA, Aryee MJ.

Nat Methods. 2018 Feb 28;15(3):155-156. doi: 10.1038/nmeth.4583. No abstract available.

PMID:
29489746
10.

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

Lareau CA, Aryee MJ.

Bioinformatics. 2018 Feb 15;34(4):672-674. doi: 10.1093/bioinformatics/btx623.

11.

The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors.

Nordor AV, Nehar-Belaid D, Richon S, Klatzmann D, Bellet D, Dangles-Marie V, Fournier T, Aryee MJ.

Epigenetics. 2017 Sep;12(9):793-803. doi: 10.1080/15592294.2017.1342912. Epub 2017 Nov 24.

12.

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.

Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK.

Nat Methods. 2017 Jun;14(6):607-614. doi: 10.1038/nmeth.4278. Epub 2017 May 1.

13.

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma.

Boulay G, Awad ME, Riggi N, Archer TC, Iyer S, Boonseng WE, Rossetti NE, Naigles B, Rengarajan S, Volorio A, Kim JC, Mesirov JP, Tamayo P, Pomeroy SL, Aryee MJ, Rivera MN.

Cancer Discov. 2017 Mar;7(3):288-301. doi: 10.1158/2159-8290.CD-16-0844. Epub 2017 Feb 17.

14.

Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer.

Desai N, Sajed D, Arora KS, Solovyov A, Rajurkar M, Bledsoe JR, Sil S, Amri R, Tai E, MacKenzie OC, Mino-Kenudson M, Aryee MJ, Ferrone CR, Berger DL, Rivera MN, Greenbaum BD, Deshpande V, Ting DT.

JCI Insight. 2017 Feb 9;2(3):e91078. doi: 10.1172/jci.insight.91078.

15.

Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.

Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M.

Mol Cell. 2016 Dec 15;64(6):1088-1101. doi: 10.1016/j.molcel.2016.11.020.

16.

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis.

Gomez-Cabrero D, Almgren M, Sjöholm LK, Hensvold AH, Ringh MV, Tryggvadottir R, Kere J, Scheynius A, Acevedo N, Reinius L, Taub MA, Montano C, Aryee MJ, Feinberg JI, Feinberg AP, Tegnér J, Klareskog L, Catrina AI, Ekström TJ.

Genome Med. 2016 Nov 22;8(1):124.

17.

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK.

Nat Biotechnol. 2016 Aug;34(8):869-74. doi: 10.1038/nbt.3620. Epub 2016 Jun 27.

18.

Open-source guideseq software for analysis of GUIDE-seq data.

Tsai SQ, Topkar VV, Joung JK, Aryee MJ.

Nat Biotechnol. 2016 May 6;34(5):483. doi: 10.1038/nbt.3534. No abstract available.

PMID:
27153277
19.

Meta-Analysis With a Continuous Covariate That Is Differentially Categorized Across Studies.

Perin J, Fischer Walker CL, Black RE, Aryee MJ.

Am J Epidemiol. 2016 Mar 1;183(5):507-14. doi: 10.1093/aje/kwv140. Epub 2016 Feb 10.

PMID:
26867775
20.

Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK.

Nature. 2015 Jul 23;523(7561):481-5. doi: 10.1038/nature14592. Epub 2015 Jun 22.

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