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Prashant Mali

Title(s)Assistant Professor, Bioengineering
SchoolAcademic Aff
Phone858-822-5794
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    Collapse Research 
    Collapse Research Activities and Funding
    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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    Collapse Bibliographic 
    Collapse Publications
    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.
    List All   |   Timeline
    1. Moreno AM, Palmer N, Alemán F, Chen G, Pla A, Jiang N, Leong Chew W, Law M, Mali P. Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy. Nat Biomed Eng. 2019 Oct; 3(10):806-816. PMID: 31332341.
      View in: PubMed
    2. Mali P. Humanizing Transcriptome Engineering. Cell. 2019 Jun 27; 178(1):8-9. PMID: 31251918.
      View in: PubMed
    3. Chen G, Katrekar D, Mali P. RNA-Guided Adenosine Deaminases: Advances and Challenges for Therapeutic RNA Editing. Biochemistry. 2019 Apr 16; 58(15):1947-1957. PMID: 30943016.
      View in: PubMed
    4. Katrekar D, Chen G, Meluzzi D, Ganesh A, Worlikar A, Shih YR, Varghese S, Mali P. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat Methods. 2019 03; 16(3):239-242. PMID: 30737497.
      View in: PubMed
    5. Deshpande A, Chen BR, Zhao L, Saddoris K, Kerr M, Zhu N, Mali P, Deshpande AJ. Investigation of Genetic Dependencies Using CRISPR-Cas9-based Competition Assays. J Vis Exp. 2019 01 07; (143). PMID: 30663717.
      View in: PubMed
    6. Parekh U, Wu Y, Zhao D, Worlikar A, Shah N, Zhang K, Mali P. 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. PMID: 30448000.
      View in: PubMed
    7. Hu M, Dailamy A, Lei XY, Parekh U, McDonald D, Kumar A, Mali P. Facile Engineering of Long-Term Culturable Ex Vivo Vascularized Tissues Using Biologically Derived Matrices. Adv Healthc Mater. 2018 12; 7(23):e1800845. PMID: 30369101.
      View in: PubMed
    8. Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. Developmental barcoding of whole mouse via homing CRISPR. Science. 2018 08 31; 361(6405). PMID: 30093604.
      View in: PubMed
    9. Ford K, McDonald D, Mali P. Functional Genomics via CRISPR-Cas. J Mol Biol. 2019 Jan 04; 431(1):48-65. PMID: 29959923.
      View in: PubMed
    10. 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. In Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation. Mol Ther. 2018 07 05; 26(7):1818-1827. PMID: 29754775.
      View in: PubMed
    11. Katrekar D, Moreno AM, Chen G, Worlikar A, Mali P. Oligonucleotide conjugated multi-functional adeno-associated viruses. Sci Rep. 2018 02 26; 8(1):3589. PMID: 29483550.
      View in: PubMed
    12. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. 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. PMID: 29452643.
      View in: PubMed
    13. Pawluk A, Chen J, Ji W, Mali P.. The future of genome editing. Cell. 2018; (173):1311-1313.
    14. 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. Corrigendum: Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2017 10 09; 8:16169. PMID: 28991237.
      View in: PubMed
    15. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun; 14(6):577-580. PMID: 28481362.
      View in: PubMed
    16. 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. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. PMID: 28319113.
      View in: PubMed
    17. Moreno AM, Mali P. Therapeutic genome engineering via CRISPR-Cas systems. Wiley Interdiscip Rev Syst Biol Med. 2017 07; 9(4). PMID: 28198142.
      View in: PubMed
    18. The malERA Refresh Consultative Panel on Basic Science and Enabling Technologies.malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication. PLOS Medicine. 2017.
    19. Parekh U, Yusupova M, Mali P.. Genome engineering in human pluripotent stem cells. Current Opinion in Chemical Engineering. 2017; (15):56-67.
    20. Katrekar D, Hu M, Mali P.. Advances in CRISPR-Cas based genome engineering. Current Opinion in Biomedical Engineering. 2017; (1):78-86.
    21. Asudani D, Yusupova M, Mali P.. Genome engineering via CRISPR-Cas systems: inserting the 'precision' in precision medicine. The Journal of Precision Medicine. 2017.
    22. Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nat Methods. 2017 02; 14(2):195-200. PMID: 27918539.
      View in: PubMed
    23. 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. Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2016 11 02; 7:13330. PMID: 27804970.
      View in: PubMed
    24. Chew WL, Tabebordbar M, Cheng JK, Mali P, Wu EY, Ng AH, Zhu K, Wagers AJ, Church GM. A multifunctional AAV-CRISPR-Cas9 and its host response. Nat Methods. 2016 10; 13(10):868-74. PMID: 27595405.
      View in: PubMed
    25. Doudna J, Mali P.. CRISPR-Cas: A laboratory manual. Cold Spring Harbor Laboratory Press. 2016.
    26. Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015 Sep; 12(9):823-6. PMID: 26167643.
      View in: PubMed
    27. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2015 Feb 18; 43(3):e21. PMID: 25414332.
      View in: PubMed
    28. 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. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21; 343(6177):1360-3. PMID: 24578530.
      View in: PubMed
    29. Yang L, Mali P, Kim-Kiselak C, Church G. CRISPR-Cas-mediated targeted genome editing in human cells. Methods Mol Biol. 2014; 1114:245-67. PMID: 24557908.
      View in: PubMed
    30. Byrne SM, Mali P, Church GM. Genome editing in human stem cells. Methods Enzymol. 2014; 546:119-38. PMID: 25398338.
      View in: PubMed
    31. Aach J, Mali P, Church GM.CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv. 2014.
    32. Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013 Oct; 10(10):957-63. PMID: 24076990.
      View in: PubMed
    33. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods. 2013 Nov; 10(11):1116-21. PMID: 24076762.
      View in: PubMed
    34. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Sep; 31(9):833-8. PMID: 23907171.
      View in: PubMed
    35. 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. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013 Oct; 41(19):9049-61. PMID: 23907390.
      View in: PubMed
    36. Kusuma S, Shen YI, Hanjaya-Putra D, Mali P, Cheng L, Gerecht S. 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. PMID: 23858432.
      View in: PubMed
    37. Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods. 2013 May; 10(5):403-6. PMID: 23503053.
      View in: PubMed
    38. DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013 Apr; 41(7):4336-43. PMID: 23460208.
      View in: PubMed
    39. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15; 339(6121):823-6. PMID: 23287722.
      View in: PubMed
    40. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. 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. PMID: 22740649.
      View in: PubMed
    41. Khatau SB, Kusuma S, Hanjaya-Putra D, Mali P, Cheng L, Lee JS, Gerecht S, Wirtz D. The differential formation of the LINC-mediated perinuclear actin cap in pluripotent and somatic cells. PLoS One. 2012; 7(5):e36689. PMID: 22574215.
      View in: PubMed
    42. Zou C, Chou BK, Dowey SN, Tsang K, Huang X, Liu CF, Smith C, Yen J, Mali P, Zhang YA, Cheng L, Ye Z. 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. PMID: 22225458.
      View in: PubMed
    43. Mali P, Cheng L. Concise review: Human cell engineering: cellular reprogramming and genome editing. Stem Cells. 2012 Jan; 30(1):75-81. PMID: 21905170.
      View in: PubMed
    44. Zou J, Mali P, Huang X, Dowey SN, Cheng L. 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. PMID: 21881051.
      View in: PubMed
    45. Chou BK, Mali P, Huang X, Ye Z, Dowey SN, Resar LM, Zou C, Zhang YA, Tong J, Cheng L. 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. PMID: 21243013.
      View in: PubMed
    46. Mali P, Wirtz D, Searson PC. Interplay of RhoA and motility in the programmed spreading of daughter cells postmitosis. Biophys J. 2010 Dec 01; 99(11):3526-34. PMID: 21112276.
      View in: PubMed
    47. Swistowski A, Peng J, Liu Q, Mali P, Rao MS, Cheng L, Zeng X. Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions. Stem Cells. 2010 Oct; 28(10):1893-904. PMID: 20715183.
      View in: PubMed
    48. 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. Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Res. 2010 Oct 01; 70(19):7662-73. PMID: 20841480.
      View in: PubMed
    49. 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. 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. PMID: 20201064.
      View in: PubMed
    50. Mali P, Ye Z, Chou BK, Yen J, Cheng L. An improved method for generating and identifying human induced pluripotent stem cells. Methods Mol Biol. 2010; 636:191-205. PMID: 20336524.
      View in: PubMed
    51. Ye Z, Zhan H, Mali P, Dowey S, Williams DM, Jang YY, Dang CV, Spivak JL, Moliterno AR, Cheng L. 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. PMID: 19797525.
      View in: PubMed
    52. 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. 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. PMID: 19540188.
      View in: PubMed
    53. Mali P, Ye Z, Hommond HH, Yu X, Lin J, Chen G, Zou J, Cheng L. Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts. Stem Cells. 2008 Aug; 26(8):1998-2005. PMID: 18511599.
      View in: PubMed
    54. Yu X, Zou J, Ye Z, Hammond H, Chen G, Tokunaga A, Mali P, Li YM, Civin C, Gaiano N, Cheng L. 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. PMID: 18462696.
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    55. Chen G, Ye Z, Yu X, Zou J, Mali P, Brodsky RA, Cheng L. 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. PMID: 18397754.
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    56. Cai L, Ye Z, Zhou BY, Mali P, Zhou C, Cheng L. Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions. Cell Res. 2007 Jan; 17(1):62-72. PMID: 17211448.
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    57. Wildt B, Mali P, Searson PC. Electrochemical template synthesis of multisegment nanowires: fabrication and protein functionalization. Langmuir. 2006 Dec 05; 22(25):10528-34. PMID: 17129026.
      View in: PubMed
    58. Mali P, Bhattacharjee N, Searson PC. Electrochemically programmed release of biomolecules and nanoparticles. Nano Lett. 2006 Jun; 6(6):1250-3. PMID: 16771589.
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    59. Mali P, Sarkar A, Lal R. Facile fabrication of microfluidic systems using electron beam lithography. Lab Chip. 2006 Feb; 6(2):310-5. PMID: 16450043.
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    60. Mali P, Lal R.The dnaSET: A novel device for single-molecule DNA sequencing. IEEE Transactions on Electron Devices. 2004; (51):2004-2012.