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Items: 14

1.

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.

Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC.

Nat Commun. 2019 Sep 6;10(1):4063. doi: 10.1038/s41467-019-11955-7.

2.

Coral: Clear and Customizable Visualization of Human Kinome Data.

Metz KS, Deoudes EM, Berginski ME, Jimenez-Ruiz I, Aksoy BA, Hammerbacher J, Gomez SM, Phanstiel DH.

Cell Syst. 2018 Sep 26;7(3):347-350.e1. doi: 10.1016/j.cels.2018.07.001. Epub 2018 Aug 29.

3.

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation.

Van Bortle K, Phanstiel DH, Snyder MP.

Genome Biol. 2017 Sep 20;18(1):180. doi: 10.1186/s13059-017-1310-3.

4.

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP.

Mol Cell. 2017 Sep 21;67(6):1037-1048.e6. doi: 10.1016/j.molcel.2017.08.006. Epub 2017 Sep 7.

5.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M.

Cell. 2015 Aug 27;162(5):1051-65. doi: 10.1016/j.cell.2015.07.048. Epub 2015 Aug 20.

6.

Mango: a bias-correcting ChIA-PET analysis pipeline.

Phanstiel DH, Boyle AP, Heidari N, Snyder MP.

Bioinformatics. 2015 Oct 1;31(19):3092-8. doi: 10.1093/bioinformatics/btv336. Epub 2015 Jun 1.

7.

Genome-wide map of regulatory interactions in the human genome.

Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP.

Genome Res. 2014 Dec;24(12):1905-17. doi: 10.1101/gr.176586.114. Epub 2014 Sep 16.

8.

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.

Phanstiel DH, Boyle AP, Araya CL, Snyder MP.

Bioinformatics. 2014 Oct;30(19):2808-10. doi: 10.1093/bioinformatics/btu379. Epub 2014 Jun 5.

9.

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

Chen R, Giliani S, Lanzi G, Mias GI, Lonardi S, Dobbs K, Manis J, Im H, Gallagher JE, Phanstiel DH, Euskirchen G, Lacroute P, Bettinger K, Moratto D, Weinacht K, Montin D, Gallo E, Mangili G, Porta F, Notarangelo LD, Pedretti S, Al-Herz W, Alfahdli W, Comeau AM, Traister RS, Pai SY, Carella G, Facchetti F, Nadeau KC, Snyder M, Notarangelo LD.

J Allergy Clin Immunol. 2013 Sep;132(3):656-664.e17. doi: 10.1016/j.jaci.2013.06.013. Epub 2013 Jul 4.

10.

Proteomics and pluripotency.

Brumbaugh J, Rose CM, Phanstiel DH, Thomson JA, Coon JJ.

Crit Rev Biochem Mol Biol. 2011 Dec;46(6):493-506. doi: 10.3109/10409238.2011.624491. Epub 2011 Oct 15. Review.

11.

Proteomic and phosphoproteomic comparison of human ES and iPS cells.

Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ.

Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699.

12.

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging.

Wenger CD, Lee MV, Hebert AS, McAlister GC, Phanstiel DH, Westphall MS, Coon JJ.

Nat Methods. 2011 Oct 2;8(11):933-5. doi: 10.1038/nmeth.1716.

13.

Higher-energy collision-activated dissociation without a dedicated collision cell.

McAlister GC, Phanstiel DH, Brumbaugh J, Westphall MS, Coon JJ.

Mol Cell Proteomics. 2011 May;10(5):O111.009456. doi: 10.1074/mcp.O111.009456. Epub 2011 Mar 10.

14.

COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA.

Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ.

Proteomics. 2011 Mar;11(6):1064-74. doi: 10.1002/pmic.201000616. Epub 2011 Feb 7.

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