Daniel Bauer

Publications

1. Direct delivery of Cas-embedded cytosine base editors as ribonucleoprotein complexes for efficient and accurate editing of clinically relevant targets. Nucleic Acids Res. 2025 Jan 07; 53(1). View Abstract
2. Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells. Cell Stem Cell. 2025 Feb 06; 32(2):191-208.e11. View Abstract
3. BCL11A +58/+55 enhancer-editing facilitates HSPC engraftment and HbF induction in rhesus macaques conditioned with a CD45 antibody-drug conjugate. Cell Stem Cell. 2025 Feb 06; 32(2):209-226.e8. View Abstract
4. Genetic medicine gestating for a-thalassemia. Blood. 2024 10 10; 144(15):1554-1556. View Abstract
5. CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing. bioRxiv. 2024 Sep 09. View Abstract
6. Scalable assessment of genome editing off-targets associated with genetic variants. bioRxiv. 2024 Jul 25. View Abstract
7. Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nat Biotechnol. 2025 Apr; 43(4):534-538. View Abstract
8. Improving prime editing with an endogenous small RNA-binding protein. Nature. 2024 Apr; 628(8008):639-647. View Abstract
9. Ex vivo culture resting time impacts transplantation outcomes of genome-edited human hematopoietic stem and progenitor cells in xenograft mouse models. Cytotherapy. 2024 06; 26(6):641-648. View Abstract
10. Direct delivery of stabilized Cas-embedded base editors achieves efficient and accurate editing of clinically relevant targets. bioRxiv. 2024 Feb 08. View Abstract
11. A viable alternative for editor delivery. Blood. 2023 08 31; 142(9):755-756. View Abstract
12. Epitope editing enables targeted immunotherapy of acute myeloid leukaemia. Nature. 2023 Sep; 621(7978):404-414. View Abstract
13. Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nat Methods. 2023 09; 20(9):1368-1378. View Abstract
14. RUNX1 mutations mitigate quiescence to promote transformation of hematopoietic progenitors in Fanconi anemia. Leukemia. 2023 08; 37(8):1698-1708. View Abstract
15. Swapping the serotype: A novel helper-dependent adenoviral vector platform for in vivo HSC gene therapy. Mol Ther Methods Clin Dev. 2023 Sep 14; 30:14-15. View Abstract
16. Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells. bioRxiv. 2023 May 27. View Abstract
17. Gene correction for sickle cell disease hits its prime. Nat Biomed Eng. 2023 05; 7(5):605-606. View Abstract
18. Pre-existing immunity does not impair the engraftment of CRISPR-Cas9-edited cells in rhesus macaques conditioned with busulfan or radiation. Mol Ther Methods Clin Dev. 2023 Jun 08; 29:483-493. View Abstract
19. Molecular Basis and Genetic Modifiers of Thalassemia. Hematol Oncol Clin North Am. 2023 04; 37(2):273-299. View Abstract
20. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun. 2023 01 13; 14(1):212. View Abstract
21. Therapeutic adenine base editing of human hematopoietic stem cells. Nat Commun. 2023 01 13; 14(1):207. View Abstract
22. Base Editing of Human Hematopoietic Stem Cells. Methods Mol Biol. 2023; 2606:43-62. View Abstract
23. Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nat Genet. 2023 Jan; 55(1):34-43. View Abstract
24. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun. 2022 12 08; 13(1):7592. View Abstract
25. Pervasive donor DNA integration defies precision gene editing of hematopoietic stem cells. Cell Stem Cell. 2022 10 06; 29(10):1426-1427. View Abstract
26. Optimization of Nuclear Localization Signal Composition Improves CRISPR-Cas12a Editing Rates in Human Primary Cells. GEN Biotechnol. 2022 Jun; 1(3):271-284. View Abstract
27. Development of a double shmiR lentivirus effectively targeting both BCL11A and ZNF410 for enhanced induction of fetal hemoglobin to treat ß-hemoglobinopathies. Mol Ther. 2022 08 03; 30(8):2693-2708. View Abstract
28. DNAJB1-PRKACA in HEK293T cells induces LINC00473 overexpression that depends on PKA signaling. PLoS One. 2022; 17(2):e0263829. View Abstract
29. Clonal hematopoiesis in sickle cell disease. Blood. 2021 11 25; 138(21):2148-2152. View Abstract
30. Editing outside the body: Ex vivo gene-modification for ß-hemoglobinopathy cellular therapy. Mol Ther. 2021 11 03; 29(11):3163-3178. View Abstract
31. Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators. Bioinformatics. 2021 Aug 09; 37(15):2103-2111. View Abstract
32. Targeting leukemia-specific dependence on the de novo purine synthesis pathway. Leukemia. 2022 02; 36(2):383-393. View Abstract
33. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet. 2021 Jun 03; 108(6):1165. View Abstract
34. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv. 2021 05 11; 5(9):2339-2349. View Abstract
35. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet. 2021 05 06; 108(5):874-893. View Abstract
36. ZNF410 represses fetal globin by singular control of CHD4. Nat Genet. 2021 05; 53(5):719-728. View Abstract
37. Author Correction: Transcription factor competition at the ?-globin promoters controls hemoglobin switching. Nat Genet. 2021 Apr; 53(4):586. View Abstract
38. Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation. Genome Med. 2021 03 10; 13(1):41. View Abstract
39. Transcription factor competition at the ?-globin promoters controls hemoglobin switching. Nat Genet. 2021 04; 53(4):511-520. View Abstract
40. Dissecting ELANE neutropenia pathogenicity by human HSC gene editing. Cell Stem Cell. 2021 05 06; 28(5):833-845.e5. View Abstract
41. BCL11A enhancer-edited hematopoietic stem cells persist in rhesus monkeys without toxicity. J Clin Invest. 2020 12 01; 130(12):6677-6687. View Abstract
42. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet. 2020 12; 52(12):1333-1345. View Abstract
43. Author Correction: Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol. 2020 Jul; 38(7):901. View Abstract
44. Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells. Cell Stem Cell. 2020 06 04; 26(6):896-909.e8. View Abstract
45. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol. 2020 07; 38(7):883-891. View Abstract
46. Therapeutic base editing of human hematopoietic stem cells. Nat Med. 2020 04; 26(4):535-541. View Abstract
47. End points for sickle cell disease clinical trials: renal and cardiopulmonary, cure, and low-resource settings. Blood Adv. 2019 12 10; 3(23):4002-4020. View Abstract
48. Gene Editing ELANE in Human Hematopoietic Stem and Progenitor Cells Reveals Disease Mechanisms and Therapeutic Strategies for Severe Congenital Neutropenia. Blood. 2019 Nov 13; 134(Supplement_1):3. View Abstract
49. Genome editing of HBG1 and HBG2 to induce fetal hemoglobin. Blood Adv. 2019 11 12; 3(21):3379-3392. View Abstract
50. Production of foetal globin in adult monkeys. Nat Biomed Eng. 2019 11; 3(11):857-859. View Abstract
51. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet. 2019 07; 51(7):1149-1159. View Abstract
52. Single-cell cloning of human T-cell lines reveals clonal variation in cell death responses to chemotherapeutics. Cancer Genet. 2019 09; 237:69-77. View Abstract
53. DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens. Bioinformatics. 2019 06 01; 35(11):1981-1984. View Abstract
54. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019 04 23; 10(1):1903. View Abstract
55. Synthetic Lethality of Wnt Pathway Activation and Asparaginase in Drug-Resistant Acute Leukemias. Cancer Cell. 2019 04 15; 35(4):664-676.e7. View Abstract
56. CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML. Nat Chem Biol. 2019 05; 15(5):529-539. View Abstract
57. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat Med. 2019 May; 25(5):776-783. View Abstract
58. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 03; 37(3):224-226. View Abstract
59. Editing aberrant splice sites efficiently restores ß-globin expression in ß-thalassemia. Blood. 2019 05 23; 133(21):2255-2262. View Abstract
60. Getting Past HSC Security: Cyclosporine H Gives Lentiviruses an Entry Pass. Cell Stem Cell. 2018 12 06; 23(6):775-776. View Abstract
61. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods. 2018 12; 15(12):992-993. View Abstract
62. FAM210B is an erythropoietin target and regulates erythroid heme synthesis by controlling mitochondrial iron import and ferrochelatase activity. J Biol Chem. 2018 12 21; 293(51):19797-19811. View Abstract
63. Emerging Genetic Therapy for Sickle Cell Disease. Annu Rev Med. 2019 01 27; 70:257-271. View Abstract
64. CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. Genome Biol. 2018 Oct 19; 19(1):169. View Abstract
65. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol. 2018 11; 36(10):977-982. View Abstract
66. AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. Bioinformatics. 2018 07 01; 34(13):i202-i210. View Abstract
67. Genetic therapies for sickle cell disease. Semin Hematol. 2018 04; 55(2):76-86. View Abstract
68. 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts. Hum Mol Genet. 2018 04 15; 27(8):1411-1420. View Abstract
69. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc. 2018 May; 13(5):946-986. View Abstract
70. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell. 2018 04 05; 173(2):430-442.e17. View Abstract
71. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell. 2018 03 12; 33(3):386-400.e5. View Abstract
72. Growing and Genetically Manipulating Human Umbilical Cord Blood-Derived Erythroid Progenitor (HUDEP) Cell Lines. Methods Mol Biol. 2018; 1698:275-284. View Abstract
73. Recent progress in understanding and manipulating haemoglobin switching for the haemoglobinopathies. Br J Haematol. 2018 03; 180(5):630-643. View Abstract
74. Curative approaches for sickle cell disease: A review of allogeneic and autologous strategies. Blood Cells Mol Dis. 2017 09; 67:155-168. View Abstract
75. Gene Therapy. Hematol Oncol Clin North Am. 2017 10; 31(5):xiii-xiv. View Abstract
76. Technical considerations for the use of CRISPR/Cas9 in hematology research. Exp Hematol. 2017 Oct; 54:4-11. View Abstract
77. An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility. J Clin Invest. 2017 Aug 01; 127(8):3065-3074. View Abstract
78. Quantitative assessment of timing, efficiency, specificity and genetic mosaicism of CRISPR/Cas9-mediated gene editing of hemoglobin beta gene in rhesus monkey embryos. Hum Mol Genet. 2017 07 15; 26(14):2678-2689. View Abstract
79. Erythropoietin signaling regulates heme biosynthesis. Elife. 2017 05 29; 6. View Abstract
80. Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PLoS Genet. 2017 04; 13(4):e1006760. View Abstract
81. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods. 2017 May 15; 121-122:118-129. View Abstract
82. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017 Apr; 49(4):625-634. View Abstract
83. Strict in vivo specificity of the Bcl11a erythroid enhancer. Blood. 2016 11 10; 128(19):2338-2342. View Abstract
84. Lineage-specific BCL11A knockdown circumvents toxicities and reverses sickle phenotype. J Clin Invest. 2016 10 03; 126(10):3868-3878. View Abstract
85. Intensive treatment and survival outcomes in NUT midline carcinoma of the head and neck. Cancer. 2016 Dec 01; 122(23):3632-3640. View Abstract
86. Forward genetic screen of human transposase genomic rearrangements. BMC Genomics. 2016 Aug 04; 17:548. View Abstract
87. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 07 12; 34(7):695-7. View Abstract
88. Fetal haemoglobin in sickle-cell disease: from genetic epidemiology to new therapeutic strategies. Lancet. 2016 Jun 18; 387(10037):2554-64. View Abstract
89. A genome editing primer for the hematologist. Blood. 2016 05 26; 127(21):2525-35. View Abstract
90. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science. 2016 Jan 15; 351(6270):285-9. View Abstract
91. Genetic treatment of a molecular disorder: gene therapy approaches to sickle cell disease. Blood. 2016 Feb 18; 127(7):839-48. View Abstract
92. Hematopoietic stem cells develop in the absence of endothelial cadherin 5 expression. Blood. 2015 Dec 24; 126(26):2811-20. View Abstract
93. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature. 2015 Nov 12; 527(7577):192-7. View Abstract
94. Hemoglobin switching's surprise: the versatile transcription factor BCL11A is a master repressor of fetal hemoglobin. Curr Opin Genet Dev. 2015 Aug; 33:62-70. View Abstract
95. Functional footprinting of regulatory DNA. Nat Methods. 2015 Oct; 12(10):927-30. View Abstract
96. EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood. 2015 Oct 15; 126(16):1930-9. View Abstract
97. miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction. Mol Ther. 2015 Sep; 23(9):1465-74. View Abstract
98. Embryonic stem cells as sources of donor-independent platelets. J Clin Invest. 2015 Jun; 125(6):2261-3. View Abstract
99. The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability. Sci Signal. 2015 Apr 14; 8(372):ra34. View Abstract
100. Generation of genomic deletions in mammalian cell lines via CRISPR/Cas9. J Vis Exp. 2015 Jan 03; (95):e52118. View Abstract
101. TMEM14C is required for erythroid mitochondrial heme metabolism. J Clin Invest. 2014 Oct; 124(10):4294-304. View Abstract
102. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem. 2014 08 01; 289(31):21312-24. View Abstract
103. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013 Oct 11; 342(6155):253-7. View Abstract
104. Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A. Proc Natl Acad Sci U S A. 2013 Apr 16; 110(16):6518-23. View Abstract
105. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell. 2012 Oct 16; 23(4):796-811. View Abstract
106. Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number. Genes Dev. 2012 Sep 15; 26(18):2075-87. View Abstract
107. Reawakening fetal hemoglobin: prospects for new therapies for the ß-globin disorders. Blood. 2012 Oct 11; 120(15):2945-53. View Abstract
108. Clinicopathologic features and long-term outcomes of NUT midline carcinoma. Clin Cancer Res. 2012 Oct 15; 18(20):5773-9. View Abstract
109. Loss-of-function and gain-of-function phenotypes of stomatocytosis mutant RhAG F65S. Am J Physiol Cell Physiol. 2011 Dec; 301(6):C1325-43. View Abstract
110. Differentiation of NUT midline carcinoma by epigenomic reprogramming. Cancer Res. 2011 Apr 01; 71(7):2686-96. View Abstract
111. Update on fetal hemoglobin gene regulation in hemoglobinopathies. Curr Opin Pediatr. 2011 Feb; 23(1):1-8. View Abstract
112. BRD4-NUT carcinoma of the mediastinum in a pediatric patient: multidetector computed tomography imaging findings. J Thorac Imaging. 2010 Aug; 25(3):W93-6. View Abstract
113. ATP citrate lyase inhibition can suppress tumor cell growth. Cancer Cell. 2005 Oct; 8(4):311-21. View Abstract
114. ATP citrate lyase is an important component of cell growth and transformation. Oncogene. 2005 Sep 15; 24(41):6314-22. View Abstract
115. The glucose dependence of Akt-transformed cells can be reversed by pharmacologic activation of fatty acid beta-oxidation. Oncogene. 2005 Jun 16; 24(26):4165-73. View Abstract
116. Growth factor regulation of autophagy and cell survival in the absence of apoptosis. Cell. 2005 Jan 28; 120(2):237-48. View Abstract
117. Cytokine stimulation of aerobic glycolysis in hematopoietic cells exceeds proliferative demand. FASEB J. 2004 Aug; 18(11):1303-5. View Abstract
118. Akt stimulates aerobic glycolysis in cancer cells. Cancer Res. 2004 Jun 01; 64(11):3892-9. View Abstract
119. Alkylating DNA damage stimulates a regulated form of necrotic cell death. Genes Dev. 2004 Jun 01; 18(11):1272-82. View Abstract
120. Bcl-x(L) complements Saccharomyces cerevisiae genes that facilitate the switch from glycolytic to oxidative metabolism. J Biol Chem. 2002 Nov 22; 277(47):44870-6. View Abstract
121. Safety and immunogenicity of ALVAC vCP1452 and recombinant gp160 in newly human immunodeficiency virus type 1-infected patients treated with prolonged highly active antiretroviral therapy. J Virol. 2002 Mar; 76(5):2206-16. View Abstract
122. Recruitment of SLP-76 to the membrane and glycolipid-enriched membrane microdomains replaces the requirement for linker for activation of T cells in T cell receptor signaling. J Exp Med. 2000 Oct 02; 192(7):1047-58. View Abstract
123. Analysis of altered gene expression by differential display. Methods Enzymol. 1995; 254:304-21. View Abstract
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