Pre-Johns Hopkins Research

  1. Kabra M, Shahi PK, Wang Y, Sinha D, Spillane A, Newby GA, Saxena S, Tong Y, Chang Y, Abdeen AA, Edwards KL, Theisen CO, Liu DR, Gamm DM, Gong S, Saha K, Pattnaik BR. “Nonviral base editing of KCNJ13 mutations preserves vision in a model of inherited retinal channelopathy”. Journal of Clinical Investigation. 2023.  
  2. Joynt AT, Kavanagh EW, Newby GA, Mitchell S, Eastman AC, Paul KC, Bowling AD, Osorio DL, Merlo CA, Patel SU, Raraigh KS, Liu DR, Sharma N, Cutting GR. “Protospacer modification improves base editing of a canonical splice site variant and recovery of CFTR function in human airway epithelia cells”. Molecular Therapy Nucleic Acids. 2023. 
  3. Mayuranathan T*, Newby GA*, Feng R, Yao Y, Mayberry KD, Lazzarotto CR, Li Y, Levine RM, Nimmagadda N, Dempsey EAD, Kang G, Porter SN, Doerfler PA, Zhang J, Jang Y, Chen J, Bell HW, Crossley M, Bhoopalan SV, Sharma A, Tisdale JF, Pruett-Miller SM, Cheng Y, Tsai SQ, Liu DR, Weiss MJ, Yen JS. “Potent and uniform fetal hemoglobin induction via base editing”. Nature Genetics. 2023. *Co-first authors. 
  4. Martin-Rufino, JD, Castano N, Pang M, Grody EI, Joubran S, Caulier A, Wahlster L, Li T, Qiu X, Riera-Escandell AM, Newby GA, Al’Khafaji A, Chaudhary S, Black S, Weng C, Munson G, Liu DR, Wlodarski MW, Sims K, Oakley JH, Fasano RM, Xavier RJ, Lander ES, Klein DE, Sankaran VG. “Massively parallel base editing to map variant effects in human hematopoiesis”. Cell. 2023.  
  5. Arbab M, Matuszek Z, Kray KM, Du A,Newby GA, Blatnik AJ, Raguram A, Richter MF, Zhao KT, Levy JM, Shen MW, Arnold WD, Wang D, Xie J, Gao G, Burghes AHM, Liu DR. “Base editing rescue of spinal muscular atrophy in cells and in mice”. Science. 2023.  
  6. Ely ZA, Mathey-Andrews N, Naranjo S, Gould SI, Mercer KL,Newby GA, Cabana CM, Rideout III WM, Jaramillo GC, Khirallah JM, Holland K, Randolph PB, Freed-Pastor WA, Davis JR, Kulstad Z, Westcott PMK, Lin A, Anzalone AV, Horton BL, Pattada NB, Shanahan S-L, Ye Z, Spranger S, Xu Q, Sanchez-Rivera FJ, Liu DR, Jacks T. “A prime editor mouse to model a broad spectrum of somatic mutations in vivo”. Nature Biotechnology. 2023.  
  7. Everette KE, Newby GA, Levine RM, Mayberry K, Jang Y, Mayuranathan T, Nimmagadda N, Dempsey E, Li Y, Bhoopalan SV, Liu X, Davis JR, Nelson AT, Chen PJ, Sousa AA, Cheng Y, Tisdale JF, Weiss MJ, Yen JS, Liu DR. “Ex vivo prime editing of patient hematopoietic stem cells rescues sickle cell disease phenotypes after engraftment in mice”. Nature Biomedical Engineering. 2023.  
  8. Davis JR, Banskota S, Levy JM, Newby GA, Wang X, Anzalone AV, Nelson AT, Chen PJ, Hennes AD, An M, Roh H, Randolph PB, Musunuru K, Liu DR. “Efficient prime editing in mouse brain, liver, and heart with dual AAVs”. Nature Biotechnology. 2023.  
  9. Li C, Georgakaopoulou A, Newby GA, Chen PJ, Everette KA, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem H-P, Liu DR, Yannaki E, Lieber A. “In vivo HSC prime editing rescues sickle cell disease in a mouse model”. Blood. 2023. (in press).  
  10. McAuley GE, Yiu G, Chang PC, Newby GA, Campo-Fernandez B, Fitz-Gibbon ST, Wu X, Kang SL, Garibay A, Butler J, Christian V, Wong RL, Everette KA, Azzun A, Gelfer H, Seet CS, Narendran A, Murguia-Favela L, Romero Z, Wright N, Liu DR, Crooks GM, Kohn DB”. Cell. 2023. Available online.  
  11. Li C, Georgakopoulou A, Newby GA, Everette KA, Nizamis E, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem H-P, Liu DR, Yannaki E, Lieber A. “In vivo base editing by a single IV vector injection for treatment of hemoglobinopathies”. Journal of Clinical Investigation Insight. 2022. 7(19):e162939. 
  12. Reichart D*, Newby GA*, Wakimoto H*, Lun M, Gorham JM, Curran JJ, Raguram A, DeLaughter DM, Conner DA, DC Marsiglia J, Kohli S, Chmatal L, Page D, Zabaleta N, Vandenberghe L, Liu DR, Seidman JG, Seidman C. “Efficient in vivo genome editing prevents hypertrophic cardiomyopathy in mice”. Nature Medicine. 2023. Available online. *Co-first authors. 
  13. Sheriff A, Guri I, Zebrowska P, Llopis-Hernandez V, Brooks IR, Tekkela S, Subramaniam K, Gebrezgabher R, Naso G, Petrova A, Balon K, Onoufriadis A, Kujawa M, Newby GA, Laczmanski L, Liu DR, McGrath JA, Jackow J. “ ABE8e adenine base editor precisely and efficiently corrects a recurrent COL7A1 nonsense mutation”. Scientific Reports. 2022, 12. 19643.  
  14. Neugebauer ME, Hsu A, Arbab M, Krasnow NA, Pandey S, Doman JL, McElroy AN, Huang TP, Raguram A, Banskota S, Newby GA, Tolar J, Osborn MJ, Liu DR. “Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity”. Nature Biotechnology. 2022, Nov 10. Available online. 
  15. Mouri K, Guo MH, de Boer CG, Lissner, MM, Harten IA, Newby GA, DeBerg HA, Platt WF, Gentili M, Liu DR, Campbell DJ, Hacohen N, Tewhey R, Ray JP. “Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells”. Nature Genetics. 2022, May 5. 54(5):603-612.  
  16. Choi EH, Suh S, Foik AT, Leinonen H, Newby GA, Gao XD, Banskota S, Hoang T, Du SW, Dong Z, Raguram A, Kohli S, Blackshaw S, Lyon DC, Liu DR, Palczewski K. “In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration”. Nature Communications. 2022, Apr 5. 13:1830.  
  17. Banskota S, Raguram A, Suh S, Du, SW, Davis JR, Choi EH, Wang X, Nielsen SC, Newby GA, Randolph PB, Osborn MJ, Musunuru K, Palczewski K, Liu DR. “Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins”. Cell. 2022, Jan 20. 185(2):250-265.  
  18. Knipping F, Newby GA, Eide CR, McElroy AN, Nielsen SC, Smith K, Fang Y, Cornu TI, Costa C, Gutierrez-Guerrero A, Bingea SP, Feser CJ, Steinbeck B, Hippen KL, Blazar BR, McCaffrey A, Mussolino C, Verhoeyen E, Tolar J, Liu DR, Osborn MJ. “Disruption of HIV-1 co-receptors CCR5 and CXCR4 in primary human T cells and hematopoietic stem and progenitor cells using base editing”. Molecular Therapy. 2022, Jan 5. 30(1):130-144.  
  19. Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen P-F, Chen C, Nelson JW, Newby GA, Sahin M, Osborn MJ, Weissman JS, Adamson B, Liu DR. “Enhanced prime editing systems by manipulating cellular determinants of editing outcomes”. Cell. 2021, Oct 28. 184(22):5635-5652.
  20. Krishnamurthy S, Traore S, Cooney AL, Brommel CM, Kulhankova K, Sinn PL, Newby GA, Liu DR, McCray PB. “Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors”. Nucleic Acids Research. 2021, Oct 11. 49(18):10558-10572. 
  21. Nelson JW, Randolph PB, Shen SP, Everette KA, Anzalone AV, Newby GA, Chen PJ, An M, Chen JC, Hsu A, Liu DR. “Engineered pegRNAs that improve prime editing efficiency”. Nature Biotechnology. 2021, Oct 4. 40:402-410.
  22. Koblan LW, Arbab M, Shen MW, Hussmann JA, Anzalone AV, Doman JL, Newby GA, Yang D, Mok B, Replogle JM, Xu A, Sisley TA, Weissman JS, Adamson B, Liu DR. “Development of C•G-to-G•C Transversion Base Editors from CRISPRi Screens, Target-Library Analysis and Machine Learning”. Nature Biotechnology. 2021, Jun 28. 39(11):1414-1425. 
  23. Newby GA*,Yen JS*, Woodard KJ*, Mayuranathan T*, Lazzarotto CR, Li Y, Sheppard-Tillman H, Porter SN, Yao Y, Mayberry K, Everette KA, Jang Y, Podracky CJ, Thaman E, Lechauve C, Sharma A, Henderson JM, Richter MF, Zhao KT, Miller SM, Wang T, Koblan LW, McCaffrey AP, Tisdale JF, Kalfa TA, Pruett-Miller PM, Tsai SQ, Weiss MJ, Liu DR. “Base editing of hematopoietic stem cells rescues sickle cell disease in mice”. Nature. 2021, Jun 2. 595:295-302. *Co-first authors.  
  24. Yeh WH, Shubina-Olenik O, Levy JM, Pan B, Newby GA, Wornow M, Burt R, Chen JC, Holt JR, Liu DR. “In vivo postnatal base editing rescues hearing in a mouse model of recessive deafness.” Science Translational Medicine. 2021, Jun 1. 12(546):eaay9101.  
  25. Petri K, Kim DY, Sasaki KE, Canver MC, Wang X, Shah H, Lee H, Horng JE, Clemenb K, Iyer S, Garcia SP, Guo JA, Newby GA, Pinello L, Liu DR, Aryee MJ, Musunuru K, Joung JK, Pattanayak V. “Global-scale CRISPR gene editor specificity profiling by ONE-seq identifies population-specific, variant off-target effects”. bioRxiv. 2021, Apr 5.  
  26. Gao P, Lyu Q, Ghanam AR, Lazzarotto CR, Newby GA, Zhang W, Choi M, Holden K, Walker II JA, Kadina AP, Munrow RJ, Abratte CM, Schmenti JC, Liu DR, Tsai SQ, Long X, Miano JM. “Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression”. Genome Biology. 2021, Mar 16. 22:83.  
  27. Koblan LW, Erdos MR, Wilson C, Cabral WA, Levy JM, Xiong Z-M, Taarez UL, Davison L, Gete YG, Mao X, Newby GA, Doherty SP, Narisu N, Sheng Q, Krilow C, Lin CY, Gordon LB, Cao K, Collins FS, Brown JD, Liu DR. “In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice”. Nature. 2021, Jan 6. 589:608-614.  
  28. Suh S, Choi EH, Leinonen H, Foik AT, Newby GA, Yeh WH, Dong Z, Kiser PD, Lyon DX, Liu DR, Palczewski K. “Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing.” Nature Biomedical Engineering. 2020, Oct 9. 5:169-178.  
  29. Tsvetkov P, Eisen TJ, Heinrich SU, Brune Z, Hallacli E, Newby GA, Kayatekin , Pincus D, Lindquist S. “Persistent Activation of mRNA translation by transient Hsp90 inhibition”. Cell Reports. 2020, Aug 11.
  30. Jiang T, Henderson JM, Coote K, Cheng Y, Valley HC, Zhange XO, Wang Q, Rhym LH, Cao Y, Newby GA, Bihler H, Mense M, Weng Z, Anderson DG, McCaffrey AP, Liu DR, Xue W. “Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope”. Nature Communications. 2020, Apr 24. 11:1979.  
  31. Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, Wilson C, Koblan LW, Zeng J, Bauer DE, Doudna JA, Liu DR. “Phage-assisted evolution of an adenine base editor with enhanced Cas domain compatibility and activity.” Nature Biotechnology. 2020, Mar 16. 38(7): 883-891.  
  32. Miller SM, Wang T, Randolph PB, Arbab M, Shen MW, Huang TP, Matuszek Z, Newby GA, Rees HA, Liu DR. “Continuous evolution of SpCas9 variants compatible with non-G PAMs.” Nature Biotechnology. 2020, Feb 10. 38(4):471-481.  
  33. Doman JL, Raguram A, Newby GA, Liu DR. “Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors.” Nature Biotechnology. 2020, Feb 10. 38(5):620-628.  
  34. Osborn MJ*, Newby GA*, Knipping F, McElroy AN, Riddle M, Xia L, Nielsen SC, Eide C, Dabelsteen S, Wandall HH, Blazar BR, Liu DR, Tolar J. “Base editor correction of COL7A1 in recessive dystrophic epidermolysis bullosa patient-derived fibroblasts and iPSCs”. Journal of Investigative Dermatology. 2020, Feb 1. 140(2):338-347. *Co-first authors 
  35. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. “Search-and-replace genome editing without double-strand breaks or donor DNA.” Nature. 2019, Oct 21. 576:149-157.  
  36. Thuronyi BW, Koblan LW, Levy JM, Yeh W, Zheng C, Newby GA, Wilson C, Bhaumik M, Shubina-Oleinik O, Holt JR, Liu DR. “Continuous evolution of base editors with expanded target compatibility and improved activity.” Nature Biotechnology. 2019, July 22. 37:1070-1079.  
  37. Fanning S, Haque A, Imberdis T, Baru V, Barrasa MI, Nuber S, Termine D, Ramalingam N, Ho GPH, Noble T, Sandoe J, Lou Y, Landgraf D, Freyzon Y, Newby GA, Soldner F, Terry-Kantor E, Kim TE, Hofbauer HF, Becuwe M, Jaenisch R, Pincus D, Clish CB, Walther TC, Farese RV, Srinivasan S, Welte MA, Kohlwein SD, Dettemer U, Lindquist S, Selkoe D. “Lipidomic Analysis of α-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment.” Molecular Cell. 2019, Mar 7. 73(5):1001:1014.  
  38. Koblan LW, Doman JL, Wilson C, Levy JM, Tay T, Newby GA, Maianti JP, Raguram A, Liu DR. “Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction.” Nature Biotechnology. 2018, Oct 1. 36: 843-846.  
  39. Newby GA*, Lindquist S. “Pioneer cells established by the [SWI+] prion can promote dispersal and out-crossing in yeast.” PLoS Biology. 2017, Nov 14. 15(11):e2003476. *Corresponding author. 
  40. Newby GA*, Kiriakov S*, Hallacli E*, Kayatekin C, Tsvetkov P, Mancuso CP, Bonner JM, Hesse WR, Chakrabortee S, Manogaran AL, Liebman SW, Lindquist S, Khalil AS. “A genetic tool to track protein aggregates and control prion inheritance.” Cell. 2017, Nov 2. 171(4):966-979. *Co-first authors.  
  41. Chakrabortee S, Kayatekin C, Newby GA, Mendillo M, Lancaster A, Lindquist S. “Luminidependens (LD): An Arabidopsis protein with prion-like behavior.” PNAS. 2016, May 24. 113(21) 6065-6070. 
  42. Schütz M, Batyuk A, Klenk C, Kummer L, de Picciotto S, Gülbakan B, Wu Y, Newby GA, Zosel F, Schöppe J, Sedlák E, Mittl PRE, Zenobi R, Wittrup KD, Plückthun A. “Generation of fluorogen-activating designed ankyrin repeat proteins (FADAs) as versatile sensor tools.” Journal of Molecular Biology. 2016, Mar 27 428(6):1272-1289.  
  43. Jarosz DF, Brown JC, Walker GA, Datta MS, Ung WL, Lancaster AK, Rotem A, Chang A, Newby GA, Weitz DA, Bisson LF, Lindquist S. “Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism.” Cell. 2014, Aug 28. 158(5):1083-1093.
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Review and Perspective Articles

  1. Newby GA*, Liu DR*. “In vivo somatic cell base editing and prime editing”. Molecular Therapy. 2021, Nov 3. 29(11):3107-3124. *Co-corresponding authors 
  2. Newby GA. “Base editing: Efficient installation of point mutations with minimal byproducts.” Stem Cells and Development. 2019, Jun 3. 28(11):712-713. 
  3. Newby GA*, Kayatekin C. “Microbial specialization by prions.” Prion. 2018, Jul 24. 12(3-4):157-161. *Co-corresponding authors. 
  4. Newby GA, Lindquist S. “Blessings in disguise: biological benefits of prion-like mechanisms.” Trends in Cell Biology. 2013, Jun 1. 23(6):251-259. 
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Guidelines/Protocols

  1.     Huang TP, Newby GA, Liu DR. “Precision Genome Editing Using Cytosine and Adenine Base Editors.” Nature Protocols. 2021, Jan 18. 16:1089-1128.