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Prashant Mali

Title(s)Associate Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Dissecting the interplay of gene regulatory networks and cellular niche on cell fate determination
    NIH/NIGMS R01GM123313May 1, 2018 - Apr 30, 2022
    Role: Principal Investigator
    Systematic mapping of genetic vulnerabilities in head and neck cancer
    NIH/NCI R01CA222826Dec 18, 2017 - Nov 30, 2022
    Role: Principal Investigator
    Next-generation Functional Genetic Screening of Un-screenable Traits
    NIH/NHGRI R01HG009285Aug 25, 2017 - Jul 31, 2021
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Translating CRISPR-Cas Therapeutics: Approaches and Challenges. CRISPR J. 2020 Aug; 3(4):253-275. Tay LS, Palmer N, Panwala R, Chew WL, Mali P. PMID: 32833535.
      View in: PubMed   Mentions: 1     Fields:    
    2. Mapping regulators of cell fate determination: Approaches and challenges. APL Bioeng. 2020 Sep; 4(3):031501. Kumar A, Mali P. PMID: 32637855.
      View in: PubMed   Mentions:
    3. CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia. Mol Ther Methods Clin Dev. 2020 Jun 12; 17:1026-1036. Rocca CJ, Rainaldi JN, Sharma J, Shi Y, Haquang JH, Luebeck J, Mali P, Cherqui S. PMID: 32462051.
      View in: PubMed   Mentions:
    4. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. Nat Biomed Eng. 2019 10; 3(10):806-816. Moreno AM, Palmer N, Alemán F, Chen G, Pla A, Jiang N, Leong Chew W, Law M, Mali P. PMID: 31332341.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    5. Humanizing Transcriptome Engineering. Cell. 2019 06 27; 178(1):8-9. Mali P. PMID: 31251918.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. RNA-Guided Adenosine Deaminases: Advances and Challenges for Therapeutic RNA Editing. Biochemistry. 2019 04 16; 58(15):1947-1957. Chen G, Katrekar D, Mali P. PMID: 30943016.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    7. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat Methods. 2019 03; 16(3):239-242. Katrekar D, Chen G, Meluzzi D, Ganesh A, Worlikar A, Shih YR, Varghese S, Mali P. PMID: 30737497.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    8. Investigation of Genetic Dependencies Using CRISPR-Cas9-based Competition Assays. J Vis Exp. 2019 01 07; (143). Deshpande A, Chen BR, Zhao L, Saddoris K, Kerr M, Zhu N, Mali P, Deshpande AJ. PMID: 30663717.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    9. Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. Cell Syst. 2018 11 28; 7(5):548-555.e8. Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. PMID: 30448000.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. Facile Engineering of Long-Term Culturable Ex Vivo Vascularized Tissues Using Biologically Derived Matrices. Adv Healthc Mater. 2018 12; 7(23):e1800845. Hu M, Dailamy A, Lei XY, Parekh U, McDonald D, Kumar A, Mali P. PMID: 30369101.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    11. Developmental barcoding of whole mouse via homing CRISPR. Science. 2018 08 31; 361(6405). Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. PMID: 30093604.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    12. Functional Genomics via CRISPR-Cas. J Mol Biol. 2019 01 04; 431(1):48-65. Ford K, McDonald D, Mali P. PMID: 29959923.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    13. In Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation. Mol Ther. 2018 07 05; 26(7):1818-1827. Moreno AM, Fu X, Zhu J, Katrekar D, Shih YV, Marlett J, Cabotaje J, Tat J, Naughton J, Lisowski L, Varghese S, Zhang K, Mali P. PMID: 29754775.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    14. Oligonucleotide conjugated multi-functional adeno-associated viruses. Sci Rep. 2018 02 26; 8(1):3589. Katrekar D, Moreno AM, Chen G, Worlikar A, Mali P. PMID: 29483550.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    15. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 02 15; 69(4):699-708.e7. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. PMID: 29452643.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    16. The future of genome editing. Cell. 2018; (173):1311-1313. Pawluk A, Chen J, Ji W, Mali P. .
    17. Corrigendum: Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2017 10 09; 8:16169. Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. PMID: 28991237.
      View in: PubMed   Mentions:    Fields:    
    18. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun; 14(6):577-580. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. PMID: 28481362.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    19. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. PMID: 28319113.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    20. Therapeutic genome engineering via CRISPR-Cas systems. Wiley Interdiscip Rev Syst Biol Med. 2017 07; 9(4). Moreno AM, Mali P. PMID: 28198142.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    21. malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication. PLOS Medicine. 2017. The malERA Refresh Consultative Panel on Basic Science and Enabling Technologies.
    22. Genome engineering in human pluripotent stem cells. Current Opinion in Chemical Engineering. 2017; (15):56-67. Parekh U, Yusupova M, Mali P. .
    23. Advances in CRISPR-Cas based genome engineering. Current Opinion in Biomedical Engineering. 2017; (1):78-86. Katrekar D, Hu M, Mali P. .
    24. Genome engineering via CRISPR-Cas systems: inserting the 'precision' in precision medicine. The Journal of Precision Medicine. 2017. Asudani D, Yusupova M, Mali P. .
    25. Rapidly evolving homing CRISPR barcodes. Nat Methods. 2017 02; 14(2):195-200. Kalhor R, Mali P, Church GM. PMID: 27918539.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    26. Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2016 11 02; 7:13330. Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. PMID: 27804970.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    27. A multifunctional AAV-CRISPR-Cas9 and its host response. Nat Methods. 2016 10; 13(10):868-74. Chew WL, Tabebordbar M, Cheng JK, Mali P, Wu EY, Ng AH, Zhu K, Wagers AJ, Church GM. PMID: 27595405.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansAnimalsCells
    28. CRISPR-Cas: A laboratory manual. Cold Spring Harbor Laboratory Press. 2016. Doudna J, Mali P. .
    29. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015 Sep; 12(9):823-6. Chari R, Mali P, Moosburner M, Church GM. PMID: 26167643.
      View in: PubMed   Mentions: 100     Fields:    Translation:HumansCells
    30. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2015 Feb 18; 43(3):e21. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. PMID: 25414332.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    31. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21; 343(6177):1360-3. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. PMID: 24578530.
      View in: PubMed   Mentions: 211     Fields:    Translation:HumansCells
    32. CRISPR-Cas-mediated targeted genome editing in human cells. Methods Mol Biol. 2014; 1114:245-67. Yang L, Mali P, Kim-Kiselak C, Church G. PMID: 24557908.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    33. Genome editing in human stem cells. Methods Enzymol. 2014; 546:119-38. Byrne SM, Mali P, Church GM. PMID: 25398338.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    34. CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv. 2014. Aach J, Mali P, Church GM.
    35. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013 Oct; 10(10):957-63. Mali P, Esvelt KM, Church GM. PMID: 24076990.
      View in: PubMed   Mentions: 410     Fields:    Translation:Cells
    36. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods. 2013 Nov; 10(11):1116-21. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. PMID: 24076762.
      View in: PubMed   Mentions: 274     Fields:    Translation:Cells
    37. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Sep; 31(9):833-8. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. PMID: 23907171.
      View in: PubMed   Mentions: 610     Fields:    Translation:HumansCells
    38. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013 Oct; 41(19):9049-61. Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. PMID: 23907390.
      View in: PubMed   Mentions: 148     Fields:    Translation:HumansCells
    39. Self-organized vascular networks from human pluripotent stem cells in a synthetic matrix. Proc Natl Acad Sci U S A. 2013 Jul 30; 110(31):12601-6. Kusuma S, Shen YI, Hanjaya-Putra D, Mali P, Cheng L, Gerecht S. PMID: 23858432.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    40. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods. 2013 May; 10(5):403-6. Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. PMID: 23503053.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    41. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013 Apr; 41(7):4336-43. DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. PMID: 23460208.
      View in: PubMed   Mentions: 407     Fields:    Translation:AnimalsCells
    42. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15; 339(6121):823-6. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. PMID: 23287722.
      View in: PubMed   Mentions: 2689     Fields:    Translation:HumansCells
    43. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 2012 Aug; 40(15):e117. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. PMID: 22740649.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansCells
    44. The differential formation of the LINC-mediated perinuclear actin cap in pluripotent and somatic cells. PLoS One. 2012; 7(5):e36689. Khatau SB, Kusuma S, Hanjaya-Putra D, Mali P, Cheng L, Lee JS, Gerecht S, Wirtz D. PMID: 22574215.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    45. Efficient derivation and genetic modifications of human pluripotent stem cells on engineered human feeder cell lines. Stem Cells Dev. 2012 Aug 10; 21(12):2298-311. Zou C, Chou BK, Dowey SN, Tsang K, Huang X, Liu CF, Smith C, Yen J, Mali P, Zhang YA, Cheng L, Ye Z. PMID: 22225458.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    46. Concise review: Human cell engineering: cellular reprogramming and genome editing. Stem Cells. 2012 Jan; 30(1):75-81. Mali P, Cheng L. PMID: 21905170.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    47. Site-specific gene correction of a point mutation in human iPS cells derived from an adult patient with sickle cell disease. Blood. 2011 Oct 27; 118(17):4599-608. Zou J, Mali P, Huang X, Dowey SN, Cheng L. PMID: 21881051.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansAnimalsCells
    48. Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Res. 2011 Mar; 21(3):518-29. Chou BK, Mali P, Huang X, Ye Z, Dowey SN, Resar LM, Zou C, Zhang YA, Tong J, Cheng L. PMID: 21243013.
      View in: PubMed   Mentions: 176     Fields:    Translation:HumansCells
    49. Interplay of RhoA and motility in the programmed spreading of daughter cells postmitosis. Biophys J. 2010 Dec 01; 99(11):3526-34. Mali P, Wirtz D, Searson PC. PMID: 21112276.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    50. Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions. Stem Cells. 2010 Oct; 28(10):1893-904. Swistowski A, Peng J, Liu Q, Mali P, Rao MS, Cheng L, Zeng X. PMID: 20715183.
      View in: PubMed   Mentions: 104     Fields:    Translation:HumansCells
    51. Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Res. 2010 Oct 01; 70(19):7662-73. Ohm JE, Mali P, Van Neste L, Berman DM, Liang L, Pandiyan K, Briggs KJ, Zhang W, Argani P, Simons B, Yu W, Matsui W, Van Criekinge W, Rassool FV, Zambidis E, Schuebel KE, Cope L, Yen J, Mohammad HP, Cheng L, Baylin SB. PMID: 20841480.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    52. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells. 2010 Apr; 28(4):713-20. Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, Brodsky RA, Ohm JE, Yu W, Baylin SB, Yusa K, Bradley A, Meyers DJ, Mukherjee C, Cole PA, Cheng L. PMID: 20201064.
      View in: PubMed   Mentions: 174     Fields:    Translation:HumansCells
    53. An improved method for generating and identifying human induced pluripotent stem cells. Methods Mol Biol. 2010; 636:191-205. Mali P, Ye Z, Chou BK, Yen J, Cheng L. PMID: 20336524.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    54. Human-induced pluripotent stem cells from blood cells of healthy donors and patients with acquired blood disorders. Blood. 2009 Dec 24; 114(27):5473-80. Ye Z, Zhan H, Mali P, Dowey S, Williams DM, Jang YY, Dang CV, Spivak JL, Moliterno AR, Cheng L. PMID: 19797525.
      View in: PubMed   Mentions: 153     Fields:    Translation:HumansAnimalsCells
    55. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell. 2009 Jul 02; 5(1):97-110. Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L. PMID: 19540188.
      View in: PubMed   Mentions: 232     Fields:    Translation:HumansCells
    56. Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts. Stem Cells. 2008 Aug; 26(8):1998-2005. Mali P, Ye Z, Hommond HH, Yu X, Lin J, Chen G, Zou J, Cheng L. PMID: 18511599.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansAnimalsCells
    57. Notch signaling activation in human embryonic stem cells is required for embryonic, but not trophoblastic, lineage commitment. Cell Stem Cell. 2008 May 08; 2(5):461-71. Yu X, Zou J, Ye Z, Hammond H, Chen G, Tokunaga A, Mali P, Li YM, Civin C, Gaiano N, Cheng L. PMID: 18462696.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    58. Trophoblast differentiation defect in human embryonic stem cells lacking PIG-A and GPI-anchored cell-surface proteins. Cell Stem Cell. 2008 Apr 10; 2(4):345-55. Chen G, Ye Z, Yu X, Zou J, Mali P, Brodsky RA, Cheng L. PMID: 18397754.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    59. Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions. Cell Res. 2007 Jan; 17(1):62-72. Cai L, Ye Z, Zhou BY, Mali P, Zhou C, Cheng L. PMID: 17211448.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    60. Electrochemical template synthesis of multisegment nanowires: fabrication and protein functionalization. Langmuir. 2006 Dec 05; 22(25):10528-34. Wildt B, Mali P, Searson PC. PMID: 17129026.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    61. Electrochemically programmed release of biomolecules and nanoparticles. . 2006 Jun; 6(6):1250-3. Mali P, Bhattacharjee N, Searson PC. PMID: 16771589.
      View in: PubMed   Mentions:
    62. Facile fabrication of microfluidic systems using electron beam lithography. Lab Chip. 2006 Feb; 6(2):310-5. Mali P, Sarkar A, Lal R. PMID: 16450043.
      View in: PubMed   Mentions: 1     Fields:    
    63. The dnaSET: A novel device for single-molecule DNA sequencing. IEEE Transactions on Electron Devices. 2004; (51):2004-2012. Mali P, Lal R.
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