Selected publications
Vinjamur DS, Yao Q, Cole MA, McGuckin C, Ren C, Zeng J, Hossain M, Luk K, Wolfe SA, Pinello L, Bauer DE. ZNF410 represses fetal globin by singular control of CHD4. Nat Genet. 2021 Apr 15. doi: 10.1038/s41588-021-00843-w. Online ahead of print. PMID: 33859416. See News&Views in Nature Genetics.
Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE*, Pinello L*. Motif-Raptor: A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators. Bioinformatics. 2021 Feb 3:btab072. PMID: 33532840.
Rao S*, Yao Y*, Soares de Brito J*, Yao Q, Shen AH, Watkinson RE, Kennedy AL, Coyne S, Ren C, Zeng J, Serbin AV, Studer S, Ballotti K, Harris CE, Luk K, Stevens CS, Armant M, Pinello L, Wolfe SA, Chiarle R, Shimamura A, Lee B, Newburger PE, Bauer DE. Dissecting ELANE neutropenia pathogenicity by human HSC gene editing. Cell Stem Cell. 2021 Jan 25:S1934-5909(20)30599-3. PMID: 33513358.
Demirci S*, Zeng J*, Wu Y, Uchida N, Shen AH, Pellin D, Gamer J, Yapundich M, Drysdale C, Bonanno J, Bonifacino AC, Krouse A, Linde NS, Engels T, Donahue RE, Haro-Mora JJ, Leonard A, Nassehi T, Luk K, Porter SN, Lazzarotto CR, Tsai SQ, Weiss M, Pruett-Miller SM, Wolfe SA, Bauer DE, Tisdale JF. BCL11A enhancer edited hematopoietic stem cells persist in rhesus monkeys without toxicity. J Clin Invest. 2020 Dec 1;130(12):6677-6687. PMID: 32897878.
Nat Med. 2020 Apr;26(4):535-541. PMID: 32284612. See Research Highlight in Nature Reviews Drug Discovery 2020.
Sher F*, Hossain M*, Seruggia D*, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet. 2019 Jul;51(7):1149-1159. PMID: 31253978.
Wu Y*, Zeng J*, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat Med. 2019 May;25(5):776-783. PMID: 30911135. See NIH Director’s Blog.
Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE*, Pinello L*. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 Mar;37(3):224-226. PMID: 30809026. Link to tool.
Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA*, Bauer DE*. Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia. Blood. 2019 May 23;133(21):2255-2262. PMID: 30704988. See Commentary in Blood.
Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE*, Pinello L*. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods. 2018 Dec;15(12):992-993. PMID: 30504875.
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. PMID: 30340514.
Lessard S*, Gatof ES*, Beaudoin M, Schupp PG, Sher F, Ali A, Prehar S, Kurita R, Nakamura Y, Baena E, Ledoux J, Oceandy D, Bauer DE*, Lettre G*. An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility. J Clin Invest. 2017 Aug 1;127(8):3065-3074. PMID: 28714864.
Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE*, Orkin SH*. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017 Apr;49(4):625-634. PMID: 28218758. See Spotlight in Trends in Genetics 33:580.
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. PMID: 27404874.
Lettre G*, Bauer DE*. Fetal haemoglobin in sickle-cell disease: from genetic epidemiology to new therapeutic strategies. Lancet. 2016 Jun 18;387(10037):2554-64. Review. PMID: 27353686.
Hoban MD, Bauer DE. A genome editing primer for the hematologist. Blood. 2016 May 26;127(21):2525-35. Review. PMID: 27053532.
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 GC, Zhang F*, Orkin SH*, Bauer DE*. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12;527(7577):192-7. PMID: 26375006.
Bauer DE*, Canver MC*, Orkin SH. Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9. J. Vis. Exp. (95), e52118, doi:10.3791/52118 (2015).
Canver MC*, Bauer DE*, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of Genomic Deletion Efficiency Mediated by CRISPR/Cas9 in Mammalian Cells. J Biol Chem 2014; Aug 1;289(31):21312-24. PMCID: 4118095. Selected as JBC Paper of the Week and as Best of JBC 2014.
Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo P, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin, SH. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013 Oct 11;342(6155):253-7. PMID: 24115442. Report Featured on Cover and Accompanied by Perspective in Science 342:206.