Selected Publications

Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L#, Bauer DE#. CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. Genome Biol. 2018 Oct
19;19(1):169. doi: 10.1186/s13059-018-1563-5.

Clement K, Farouni R, Bauer DE, Pinello L. AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics. 2018 Jul 1;34(13):i202-i210. doi: 10.1093/bioinformatics/bty264.

Canver MC*,  Haeussler M*, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP & Pinello L. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protocols. 2018 May;13(5):946-986. doi: 10.1038/nprot.2018.005

Canver MC, Joung JK, Pinello L. Impact of Genetic Variation on CRISPR-Cas Targeting. The CRISPR Journal. 2018 Apr 1;1(2):159-170. doi: 10.1089/crispr.2017.0016

Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK#, Aryee MJ#, Pinello L#. Response to “Unexpected mutations after CRISPR-Cas9 editing in vivo”. Nat Methods. 2018 Apr;15(4):238-239. doi: 10.1038/nmeth.4541.

Pinello L*#, Farouni R*, Yuan GC#. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics. 2018 Jan 17. doi: 10.1093/bioinformatics/bty031.

Beyaz S*, Kim JH*, Pinello L*, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, Orkin SH, Winau F. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol. 2017 Feb;18(2):184-195. doi: 10.1038/ni.3644.

Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 Jul 12;34(7):695-7. doi: 10.1038/nbt.3583.

Guo G*, Pinello L*, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC, Orkin SH. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. Cell Rep. 2016 Feb 2;14(4):956-65. doi: 10.1016/j.celrep.2015.12.089.

Canver MC*, Smith EC*, Sher F*, Pinello L*, Sanjana NE*, Shalem O, Chen DD, Schupp PG, Vinjamur DS,  Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan G-C, Zhang F, Orkin SH & Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12;527(7577):192-72015 Sep 16. doi: 10.1038/nature15521.

Wu JN*, Pinello L*, Yissachar E, Wischhusen JW, Yuan GC, Roberts CW. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin. 2015 Dec 2;8:53. doi: 10.1186/s13072-015-0046-0.

Pinello L, Lo Bosco G, Yuan GC. Applications of alignment-free methods in epigenomics. Brief Bioinform. 2014 May;15(3):419-30. doi: 10.1093/bib/bbt078.

Pinello L*, Xu J*, Orkin SH, Yuan GC. Analysis of chromatin state plasticity identifies cell-type specific regulators of H3K27me3 patterns, PNAS. 2014 Jan 21;111(3):E344-53. doi: 10.1073/pnas.1322570111.

Pulakanti K*, Pinello L*, Stelloh C, Blinka S, Allred J, Milanovich S, Kiblawi S, Peterson J, Wang A, Yuan GC, Rao S. Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions. Epigenetics. 2013 Oct 17;8(12):1303-20. doi: 10.4161/epi.26597.

Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12(1):408. doi: 10.1186/1471-2105-12-408.

Sala A*, Toto M*, Pinello L*, Gabriele A, Di Benedetto V, Ingrassia AM, Lo Bosco G, Di Gesù V, Giancarlo R, Corona DFV. Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI. EMBO J. 2011 May 4;30(9):1766-77. doi: 10.1038/emboj.2011.98.

* co-first authors
# co-corresponding authors

For a list of all publications click here